Starting phenix.real_space_refine on Sat Mar 7 06:45:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vbp_31884/03_2026/7vbp_31884.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbp_31884/03_2026/7vbp_31884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vbp_31884/03_2026/7vbp_31884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbp_31884/03_2026/7vbp_31884.map" model { file = "/net/cci-nas-00/data/ceres_data/7vbp_31884/03_2026/7vbp_31884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbp_31884/03_2026/7vbp_31884.cif" } resolution = 2.8 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= 0.002 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 284 5.16 5 C 25352 2.51 5 N 6212 2.21 5 O 7147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39022 Number of models: 1 Model: "" Number of chains: 61 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: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 600 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "b" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 879 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 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: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4761 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "m" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 939 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 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: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1022 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "w" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2586 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 143 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "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: "g" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 114 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "l" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 245 Unusual residues: {'CDL': 2, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 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: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 245 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "S" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "j" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "k" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 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: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "s" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "w" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.50 Time building chain proxies: 8.54, per 1000 atoms: 0.22 Number of scatterers: 39022 At special positions: 0 Unit cell: (181.54, 190.133, 139.646, 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 284 16.00 P 27 15.00 O 7147 8.00 N 6212 7.00 C 25352 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=2.06 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=2.02 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 3.7 seconds 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8814 Finding SS restraints... Secondary structure from input PDB file: 221 helices and 6 sheets defined 71.1% alpha, 0.9% 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 'S' and resid 1 through 4 Processing helix chain 'S' and resid 5 through 31 Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 42 through 56 removed outlier: 3.698A pdb=" N ASN S 46 " --> pdb=" O SER S 42 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 Processing helix chain 'U' and resid 3 through 14 Processing helix chain 'U' and resid 16 through 32 Processing helix chain 'U' and resid 33 through 35 No H-bonds generated for 'chain 'U' and resid 33 through 35' Processing helix chain 'U' and resid 38 through 48 Processing helix chain 'U' and resid 78 through 84 Processing helix chain 'V' and resid 3 through 12 removed outlier: 4.021A pdb=" N ILE V 12 " --> pdb=" O LYS V 8 " (cutoff:3.500A) 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: 3.902A pdb=" N TYR V 90 " --> pdb=" O ASP V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 132 Processing helix chain 'W' and resid 33 through 98 Proline residue: W 73 - end of helix Processing helix chain 'W' and resid 99 through 101 No H-bonds generated for 'chain 'W' and resid 99 through 101' Processing helix chain 'W' and resid 120 through 126 removed outlier: 3.783A pdb=" N LEU W 124 " --> pdb=" O MET W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 129 through 143 removed outlier: 6.279A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 89 Processing helix chain 'X' and resid 94 through 98 Processing helix chain 'X' and resid 111 through 127 Processing helix chain 'X' and resid 131 through 136 Processing helix chain 'X' and resid 140 through 153 Processing helix chain 'Y' and resid 51 through 76 removed outlier: 3.676A pdb=" N LEU Y 55 " --> pdb=" O THR Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 82 Processing helix chain 'Y' and resid 88 through 92 Processing helix chain 'Y' and resid 93 through 98 Processing helix chain 'Z' and resid 18 through 22 Processing helix chain 'Z' and resid 27 through 38 removed outlier: 3.699A pdb=" N THR Z 31 " --> pdb=" O THR Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 54 removed outlier: 3.527A pdb=" N ALA Z 50 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG Z 52 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER Z 54 " --> pdb=" O TRP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 68 Processing helix chain 'Z' and resid 70 through 90 Processing helix chain 'a' and resid 61 through 93 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 108 through 113 removed outlier: 3.854A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) removed outlier: 3.727A 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: 4.097A pdb=" N ASN a 132 " --> pdb=" O GLY a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 179 removed outlier: 3.524A pdb=" N ILE a 179 " --> pdb=" O LYS a 176 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 26 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: 3.687A 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 82 through 86 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: 4.303A pdb=" N TYR d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) removed outlier: 4.583A 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: 3.870A 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 176 Processing helix chain 'e' and resid 65 through 70 removed outlier: 4.317A pdb=" N LYS e 69 " --> pdb=" O ASN e 65 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN e 70 " --> pdb=" O LEU e 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 65 through 70' Processing helix chain 'e' and resid 79 through 95 Processing helix chain 'e' and resid 97 through 108 removed outlier: 3.773A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 114 through 133 Processing helix chain 'e' and resid 143 through 147 Processing helix chain 'f' and resid 40 through 73 Processing helix chain 'g' and resid 18 through 23 Processing helix chain 'g' and resid 30 through 51 Processing helix chain 'g' and resid 59 through 99 Processing helix chain 'g' and resid 100 through 103 Processing helix chain 'g' and resid 110 through 114 Processing helix chain 'h' and resid 5 through 11 Processing helix chain 'h' and resid 15 through 19 removed outlier: 3.641A pdb=" N THR h 19 " --> pdb=" O ARG h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 29 Processing helix chain 'h' and resid 33 through 44 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 'i' and resid 2 through 23 Processing helix chain 'i' and resid 25 through 45 removed outlier: 3.624A 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: 4.077A 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: 3.682A 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: 3.590A 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: 3.525A pdb=" N THR i 241 " --> pdb=" O MET i 237 " (cutoff:3.500A) Processing helix chain 'i' and resid 259 through 272 removed outlier: 4.461A pdb=" N LYS i 263 " --> pdb=" O GLY i 259 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 301 removed outlier: 4.383A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 315 removed outlier: 3.823A pdb=" N LYS i 314 " --> pdb=" O ASN i 310 " (cutoff:3.500A) Processing helix chain 'i' and resid 325 through 335 Processing helix chain 'i' and resid 336 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 24 Processing helix chain 'j' and resid 25 through 27 No H-bonds generated for 'chain 'j' and resid 25 through 27' Processing helix chain 'j' and resid 52 through 73 removed outlier: 4.225A pdb=" N PHE j 56 " --> pdb=" O SER j 52 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 79 removed outlier: 3.583A pdb=" N SER j 79 " --> pdb=" O LEU j 75 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 108 Processing helix chain 'k' and resid 2 through 22 removed outlier: 3.793A pdb=" N MET k 6 " --> pdb=" O PRO k 2 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR k 22 " --> pdb=" O GLY k 18 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 51 Processing helix chain 'k' and resid 54 through 56 No H-bonds generated for 'chain 'k' and resid 54 through 56' Processing helix chain 'k' and resid 57 through 86 removed outlier: 4.696A 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: 3.991A pdb=" N SER l 6 " --> pdb=" O ASN l 2 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR l 8 " --> pdb=" O PHE l 4 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU l 9 " --> pdb=" O ALA l 5 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 21 Processing helix chain 'l' and resid 22 through 24 No H-bonds generated for 'chain 'l' and resid 22 through 24' Processing helix chain 'l' and resid 25 through 29 Processing helix chain 'l' and resid 31 through 58 removed outlier: 4.501A 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: 3.897A 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: 3.501A pdb=" N ASN l 165 " --> pdb=" O ARG l 161 " (cutoff:3.500A) removed outlier: 4.058A 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 225 removed outlier: 4.270A pdb=" N LEU l 213 " --> pdb=" O PRO l 209 " (cutoff:3.500A) Processing helix chain 'l' and resid 226 through 230 removed outlier: 3.719A 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 Processing helix chain 'l' and resid 297 through 319 Processing helix chain 'l' and resid 321 through 350 removed outlier: 3.753A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 355 through 359 Processing helix chain 'l' and resid 366 through 382 Processing helix chain 'l' and resid 388 through 401 removed outlier: 4.775A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 405 through 432 removed outlier: 3.544A pdb=" N LEU l 432 " --> pdb=" O PHE l 428 " (cutoff:3.500A) Processing helix chain 'l' and resid 447 through 472 removed outlier: 3.645A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.440A 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: 3.623A 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 Processing helix chain 'l' and resid 556 through 562 removed outlier: 3.900A 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 Processing helix chain 'm' and resid 4 through 22 removed outlier: 3.536A pdb=" N SER m 22 " --> pdb=" O VAL m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 48 removed outlier: 3.565A pdb=" N GLY m 29 " --> pdb=" O SER m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 75 removed outlier: 3.891A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.843A 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: 4.532A 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 33 Processing helix chain 'o' and resid 15 through 19 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 Processing helix chain 'p' and resid 64 through 74 Processing helix chain 'p' and resid 92 through 96 removed outlier: 3.502A pdb=" N GLU p 95 " --> pdb=" O GLU p 92 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N CYS p 96 " --> pdb=" O ARG p 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 92 through 96' Processing helix chain 'p' and resid 100 through 107 Processing helix chain 'p' and resid 108 through 114 removed outlier: 3.888A pdb=" N MET p 114 " --> pdb=" O SER p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 115 through 144 removed outlier: 3.577A pdb=" N PHE p 119 " --> pdb=" O TYR p 115 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.980A 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: 4.129A 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 42 No H-bonds generated for 'chain 'r' and resid 40 through 42' Processing helix chain 'r' and resid 61 through 81 removed outlier: 4.075A pdb=" N LEU r 65 " --> pdb=" O LEU r 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 88 through 112 removed outlier: 3.585A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 114 through 125 Processing helix chain 'r' and resid 125 through 136 removed outlier: 3.819A pdb=" N THR r 129 " --> pdb=" O THR r 125 " (cutoff:3.500A) Processing helix chain 'r' and resid 141 through 172 removed outlier: 3.909A 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: 4.466A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 223 removed outlier: 3.968A 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: 4.181A 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 278 removed outlier: 4.694A pdb=" N TYR r 259 " --> pdb=" O ASN r 255 " (cutoff:3.500A) Proline residue: r 260 - end of helix removed outlier: 4.090A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG r 278 " --> pdb=" O SER r 274 " (cutoff:3.500A) Processing helix chain 'r' and resid 281 through 304 Processing helix chain 'r' and resid 305 through 338 removed outlier: 3.688A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 347 through 352 removed outlier: 4.084A 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: 4.352A pdb=" N LEU r 395 " --> pdb=" O ILE r 391 " (cutoff:3.500A) Processing helix chain 'r' and resid 430 through 448 Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 449 through 455 removed outlier: 6.523A pdb=" N LYS r 452 " --> pdb=" O LEU r 449 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU r 455 " --> pdb=" O LYS r 452 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.901A 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: 4.324A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 125 through 155 removed outlier: 3.919A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 169 removed outlier: 3.761A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) Processing helix chain 's' and resid 173 through 178 removed outlier: 4.027A pdb=" N THR s 177 " --> pdb=" O TRP s 173 " (cutoff:3.500A) Processing helix chain 's' and resid 178 through 193 removed outlier: 3.584A 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 252 through 277 Processing helix chain 's' and resid 281 through 312 removed outlier: 4.857A pdb=" N LEU s 294 " --> pdb=" O TRP s 290 " (cutoff:3.500A) Proline residue: s 295 - end of helix Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 10 through 14 Processing helix chain 'u' and resid 21 through 36 removed outlier: 4.880A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 36 through 51 removed outlier: 3.537A 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: 3.576A pdb=" N SER u 92 " --> pdb=" O CYS u 88 " (cutoff:3.500A) Processing helix chain 'u' and resid 100 through 116 removed outlier: 3.537A 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 26 through 30 removed outlier: 4.185A pdb=" N GLY v 30 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing helix chain 'v' and resid 42 through 49 Processing helix chain 'v' and resid 59 through 73 removed outlier: 3.501A pdb=" N LEU v 63 " --> pdb=" O CYS v 59 " (cutoff:3.500A) Processing helix chain 'v' and resid 81 through 125 Processing helix chain 'w' and resid 39 through 46 Processing helix chain 'w' and resid 69 through 82 Processing helix chain 'w' and resid 92 through 98 removed outlier: 3.585A pdb=" N SER w 96 " --> pdb=" O HIS w 92 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR w 97 " --> pdb=" O TYR w 93 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR w 98 " --> pdb=" O ALA w 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 92 through 98' Processing helix chain 'w' and resid 113 through 120 Processing helix chain 'w' and resid 126 through 154 Processing helix chain 'w' and resid 166 through 176 removed outlier: 4.010A pdb=" N LEU w 170 " --> pdb=" O ASP w 166 " (cutoff:3.500A) Processing helix chain 'w' and resid 180 through 196 removed outlier: 3.564A pdb=" N VAL w 184 " --> pdb=" O ARG w 180 " (cutoff:3.500A) Processing helix chain 'w' and resid 210 through 222 removed outlier: 3.779A pdb=" N GLY w 222 " --> pdb=" O ILE w 218 " (cutoff:3.500A) Processing helix chain 'w' and resid 225 through 229 removed outlier: 3.578A pdb=" N ILE w 229 " --> pdb=" O GLU w 226 " (cutoff:3.500A) Processing helix chain 'w' and resid 230 through 243 removed outlier: 3.553A pdb=" N LEU w 234 " --> pdb=" O THR w 230 " (cutoff:3.500A) Processing helix chain 'w' and resid 245 through 251 Processing helix chain 'w' and resid 265 through 276 removed outlier: 4.054A pdb=" N VAL w 269 " --> pdb=" O ASP w 265 " (cutoff:3.500A) Processing helix chain 'w' and resid 282 through 286 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: 3.963A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE w 310 " --> pdb=" O TYR w 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 310' Processing helix chain 'w' and resid 320 through 333 Processing helix chain 'w' and resid 351 through 355 Processing sheet with id=AA1, first strand: chain 'U' and resid 57 through 58 removed outlier: 6.871A 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 98 removed outlier: 7.395A pdb=" N ASN l 65 " --> pdb=" O PHE l 80 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N PHE l 80 " --> pdb=" O ASN l 65 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N HIS l 67 " --> pdb=" O LEU l 78 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU l 78 " --> pdb=" O HIS l 67 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET l 69 " --> pdb=" O LEU l 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'i' and resid 307 through 308 Processing sheet with id=AA5, first strand: chain 'r' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'w' and resid 84 through 86 removed outlier: 6.425A pdb=" N ARG w 84 " --> pdb=" O VAL w 158 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR w 61 " --> pdb=" O VAL w 205 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL w 207 " --> pdb=" O THR w 61 " (cutoff:3.500A) 2317 hydrogen bonds defined for protein. 6732 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: 6.74 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 7160 1.33 - 1.48: 14755 1.48 - 1.63: 17203 1.63 - 1.78: 59 1.78 - 1.93: 496 Bond restraints: 39673 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C18 UQ s 402 " pdb=" C19 UQ s 402 " ideal model delta sigma weight residual 1.336 1.556 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CA7 CDL a 201 " pdb=" OA8 CDL a 201 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CB7 CDL a 201 " pdb=" OB8 CDL a 201 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.18e+02 bond pdb=" CA7 CDL g 202 " pdb=" OA8 CDL g 202 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.17e+02 ... (remaining 39668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.81: 53336 4.81 - 9.62: 237 9.62 - 14.43: 31 14.43 - 19.23: 9 19.23 - 24.04: 2 Bond angle restraints: 53615 Sorted by residual: angle pdb=" N PRO Q 63 " pdb=" CD PRO Q 63 " pdb=" CG PRO Q 63 " ideal model delta sigma weight residual 103.20 83.39 19.81 1.50e+00 4.44e-01 1.74e+02 angle pdb=" CA PRO Q 63 " pdb=" CB PRO Q 63 " pdb=" CG PRO Q 63 " ideal model delta sigma weight residual 104.50 80.46 24.04 1.90e+00 2.77e-01 1.60e+02 angle pdb=" CA CYS V 95 " pdb=" CB CYS V 95 " pdb=" SG CYS V 95 " ideal model delta sigma weight residual 114.40 130.29 -15.89 2.30e+00 1.89e-01 4.77e+01 angle pdb=" C51 CDL r 504 " pdb=" CB5 CDL r 504 " pdb=" OB6 CDL r 504 " ideal model delta sigma weight residual 111.33 120.24 -8.91 1.32e+00 5.72e-01 4.55e+01 angle pdb=" C11 CDL l 701 " pdb=" CA5 CDL l 701 " pdb=" OA6 CDL l 701 " ideal model delta sigma weight residual 111.33 120.21 -8.88 1.32e+00 5.72e-01 4.52e+01 ... (remaining 53610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 23279 34.83 - 69.66: 742 69.66 - 104.49: 69 104.49 - 139.32: 13 139.32 - 174.15: 15 Dihedral angle restraints: 24118 sinusoidal: 10480 harmonic: 13638 Sorted by residual: dihedral pdb=" CB CYS V 95 " pdb=" SG CYS V 95 " pdb=" SG CYS V 115 " pdb=" CB CYS V 115 " ideal model delta sinusoidal sigma weight residual -86.00 -17.54 -68.46 1 1.00e+01 1.00e-02 6.08e+01 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 93.00 159.42 -66.42 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CA MET s 91 " pdb=" C MET s 91 " pdb=" N PRO s 92 " pdb=" CA PRO s 92 " ideal model delta harmonic sigma weight residual 0.00 -34.64 34.64 0 5.00e+00 4.00e-02 4.80e+01 ... (remaining 24115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 5330 0.078 - 0.157: 476 0.157 - 0.235: 21 0.235 - 0.313: 3 0.313 - 0.392: 4 Chirality restraints: 5834 Sorted by residual: chirality pdb=" C6 PLX a 202 " pdb=" C7 PLX a 202 " pdb=" O6 PLX a 202 " pdb=" O7 PLX a 202 " both_signs ideal model delta sigma weight residual False 2.01 2.40 -0.39 2.00e-01 2.50e+01 3.84e+00 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 2.33 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 5831 not shown) Planarity restraints: 6564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 402 " -0.424 2.00e-02 2.50e+03 4.60e-01 2.64e+03 pdb=" C11 UQ s 402 " -0.087 2.00e-02 2.50e+03 pdb=" C7 UQ s 402 " -0.543 2.00e-02 2.50e+03 pdb=" C8 UQ s 402 " 0.631 2.00e-02 2.50e+03 pdb=" C9 UQ s 402 " 0.422 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 402 " 0.187 2.00e-02 2.50e+03 2.19e-01 6.01e+02 pdb=" C13 UQ s 402 " -0.123 2.00e-02 2.50e+03 pdb=" C14 UQ s 402 " -0.354 2.00e-02 2.50e+03 pdb=" C15 UQ s 402 " 0.037 2.00e-02 2.50e+03 pdb=" C16 UQ s 402 " 0.252 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " -0.119 2.00e-02 2.50e+03 1.86e-01 4.31e+02 pdb=" C18 UQ s 402 " 0.043 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " 0.337 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " -0.062 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " -0.198 2.00e-02 2.50e+03 ... (remaining 6561 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 162 2.37 - 3.00: 20797 3.00 - 3.64: 59925 3.64 - 4.27: 95301 4.27 - 4.90: 157065 Nonbonded interactions: 333250 Sorted by model distance: nonbonded pdb=" OE2 GLU l 397 " pdb=" O HOH l 801 " model vdw 1.741 3.040 nonbonded pdb=" O ILE w 66 " pdb=" O2A ADP w 401 " model vdw 1.807 3.040 nonbonded pdb=" OH TYR Q 53 " pdb=" O3 PEE Q 101 " model vdw 1.845 3.040 nonbonded pdb=" O HOH i 417 " pdb=" O HOH i 420 " model vdw 1.903 3.040 nonbonded pdb=" OE2 GLU a 95 " pdb=" O1 CDL a 201 " model vdw 1.903 3.040 ... (remaining 333245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.430 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: 0.050 Extract box with map and model: 1.320 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 33.640 Find NCS groups from input model: 0.460 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: 0.010 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.264 39680 Z= 0.394 Angle : 0.904 24.042 53627 Z= 0.454 Chirality : 0.046 0.392 5834 Planarity : 0.009 0.460 6564 Dihedral : 17.166 174.151 15286 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.68 % Rotamer: Outliers : 0.32 % Allowed : 0.22 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.12), residues: 4586 helix: 1.53 (0.09), residues: 2961 sheet: -1.17 (1.11), residues: 26 loop : -0.48 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG u 47 TYR 0.024 0.002 TYR b 88 PHE 0.037 0.002 PHE s 270 TRP 0.053 0.002 TRP l 68 HIS 0.010 0.001 HIS l 56 Details of bonding type rmsd covalent geometry : bond 0.00755 (39673) covalent geometry : angle 0.90145 (53615) SS BOND : bond 0.01425 ( 6) SS BOND : angle 4.80852 ( 12) hydrogen bonds : bond 0.13098 ( 2317) hydrogen bonds : angle 5.55839 ( 6732) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 730 time to evaluate : 1.550 Fit side-chains REVERT: Q 63 PRO cc_start: 0.8021 (OUTLIER) cc_final: 0.7747 (Cg_exo) REVERT: l 397 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7515 (mt-10) REVERT: v 29 TYR cc_start: 0.7860 (t80) cc_final: 0.7556 (t80) REVERT: v 106 ARG cc_start: 0.7686 (ttp-170) cc_final: 0.7435 (ptm160) outliers start: 13 outliers final: 5 residues processed: 737 average time/residue: 0.8719 time to fit residues: 753.7244 Evaluate side-chains 612 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 606 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 63 PRO Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain w residue 61 THR Chi-restraints excluded: chain w residue 62 VAL Chi-restraints excluded: chain w residue 242 LYS Chi-restraints excluded: chain w residue 243 LYS 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: 3.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 52 ASN Z 21 GLN Z 33 GLN b 83 HIS c 164 ASN d 54 GLN d 134 GLN e 145 ASN f 61 GLN l 59 GLN l 205 ASN l 351 ASN l 405 ASN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 26 ASN r 144 ASN r 192 ASN r 366 ASN s 47 GLN u 64 ASN u 73 GLN v 4 HIS v 65 GLN w 132 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.127114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.095263 restraints weight = 45957.716| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.48 r_work: 0.2802 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 39680 Z= 0.215 Angle : 0.685 11.931 53627 Z= 0.345 Chirality : 0.046 0.202 5834 Planarity : 0.006 0.077 6564 Dihedral : 16.383 164.766 6161 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 1.99 % Allowed : 8.12 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.12), residues: 4586 helix: 1.74 (0.09), residues: 2983 sheet: -0.64 (1.13), residues: 25 loop : -0.46 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 59 TYR 0.027 0.002 TYR r 406 PHE 0.030 0.002 PHE i 292 TRP 0.034 0.002 TRP l 68 HIS 0.009 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00518 (39673) covalent geometry : angle 0.68393 (53615) SS BOND : bond 0.01104 ( 6) SS BOND : angle 2.65946 ( 12) hydrogen bonds : bond 0.06561 ( 2317) hydrogen bonds : angle 4.51733 ( 6732) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 640 time to evaluate : 1.605 Fit side-chains REVERT: S 4 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7517 (mm-30) REVERT: X 150 ASP cc_start: 0.8172 (m-30) cc_final: 0.7880 (m-30) REVERT: Y 102 ASP cc_start: 0.6135 (OUTLIER) cc_final: 0.5307 (m-30) REVERT: a 72 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8341 (ttm-80) REVERT: d 60 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8290 (tpm170) REVERT: e 151 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6585 (mp0) REVERT: i 48 PHE cc_start: 0.7613 (t80) cc_final: 0.7319 (t80) REVERT: i 299 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8369 (p) REVERT: j 16 LEU cc_start: 0.7858 (tt) cc_final: 0.7354 (tp) REVERT: l 351 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8680 (m110) REVERT: l 493 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7687 (p) REVERT: l 496 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7597 (ttt) REVERT: m 57 PHE cc_start: 0.8626 (t80) cc_final: 0.8377 (t80) REVERT: m 128 TYR cc_start: 0.5813 (m-80) cc_final: 0.5587 (m-80) REVERT: p 123 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: r 103 GLN cc_start: 0.9434 (OUTLIER) cc_final: 0.8873 (tt0) REVERT: s 227 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7763 (mm-30) REVERT: u 17 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: w 63 ASP cc_start: 0.8174 (m-30) cc_final: 0.7897 (m-30) REVERT: w 241 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.6538 (t80) outliers start: 81 outliers final: 30 residues processed: 675 average time/residue: 0.8414 time to fit residues: 671.8387 Evaluate side-chains 657 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 615 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Y residue 102 ASP Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain i residue 304 MET Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 267 MET Chi-restraints excluded: chain l residue 351 ASN Chi-restraints excluded: chain l residue 371 THR Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 495 ILE Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 28 GLU Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 123 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 120 optimal weight: 4.9990 chunk 441 optimal weight: 4.9990 chunk 10 optimal weight: 0.0870 chunk 442 optimal weight: 7.9990 chunk 437 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 360 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 158 optimal weight: 0.1980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 74 GLN Z 33 GLN c 164 ASN d 134 GLN e 148 GLN f 61 GLN l 405 ASN r 304 GLN u 64 ASN v 65 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.132255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.102785 restraints weight = 45661.433| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.35 r_work: 0.2882 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 39680 Z= 0.121 Angle : 0.559 8.728 53627 Z= 0.281 Chirality : 0.040 0.184 5834 Planarity : 0.005 0.065 6564 Dihedral : 15.202 156.471 6148 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 1.94 % Allowed : 10.01 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.13), residues: 4586 helix: 2.13 (0.09), residues: 2970 sheet: -0.61 (1.17), residues: 26 loop : -0.43 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 59 TYR 0.024 0.001 TYR r 406 PHE 0.027 0.001 PHE i 292 TRP 0.022 0.001 TRP l 144 HIS 0.007 0.001 HIS p 76 Details of bonding type rmsd covalent geometry : bond 0.00249 (39673) covalent geometry : angle 0.55864 (53615) SS BOND : bond 0.00714 ( 6) SS BOND : angle 1.89627 ( 12) hydrogen bonds : bond 0.04943 ( 2317) hydrogen bonds : angle 4.22326 ( 6732) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 650 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: V 138 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: a 72 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8280 (ttm-80) REVERT: d 36 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8323 (mt) REVERT: d 60 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8225 (tpm170) REVERT: e 64 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7110 (tt0) REVERT: e 146 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8198 (mtmm) REVERT: h 6 VAL cc_start: 0.9286 (t) cc_final: 0.8921 (m) REVERT: h 53 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8064 (tt0) REVERT: i 48 PHE cc_start: 0.7610 (t80) cc_final: 0.7334 (t80) REVERT: j 16 LEU cc_start: 0.7861 (tt) cc_final: 0.7412 (tp) REVERT: j 17 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7879 (mp) REVERT: j 90 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.9132 (mmm) REVERT: l 320 ASN cc_start: 0.8048 (t0) cc_final: 0.7774 (t0) REVERT: l 493 VAL cc_start: 0.7906 (OUTLIER) cc_final: 0.7551 (p) REVERT: l 496 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7509 (ttt) REVERT: m 57 PHE cc_start: 0.8588 (t80) cc_final: 0.8362 (t80) REVERT: n 46 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8257 (tmtt) REVERT: o 111 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8485 (mtmp) REVERT: p 123 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: p 135 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7152 (ttm110) REVERT: p 144 THR cc_start: 0.7932 (t) cc_final: 0.7670 (m) REVERT: r 103 GLN cc_start: 0.9366 (OUTLIER) cc_final: 0.8754 (tt0) REVERT: u 17 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7098 (mm-30) REVERT: v 29 TYR cc_start: 0.8039 (t80) cc_final: 0.7678 (t80) REVERT: v 72 ASP cc_start: 0.7879 (m-30) cc_final: 0.7659 (m-30) REVERT: w 176 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: w 241 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.7044 (t80) outliers start: 79 outliers final: 18 residues processed: 684 average time/residue: 0.8321 time to fit residues: 673.6851 Evaluate side-chains 644 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 607 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Z residue 21 GLN Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 28 GLU Chi-restraints excluded: chain o residue 111 LYS Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 176 GLN Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 50 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 342 optimal weight: 2.9990 chunk 452 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 381 optimal weight: 4.9990 chunk 430 optimal weight: 8.9990 chunk 278 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 74 GLN Z 33 GLN c 164 ASN d 134 GLN e 145 ASN f 61 GLN g 14 GLN l 351 ASN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 75 ASN r 304 GLN r 415 GLN u 64 ASN v 65 GLN w 202 HIS w 300 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.095424 restraints weight = 45652.857| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.32 r_work: 0.2809 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 39680 Z= 0.201 Angle : 0.646 10.870 53627 Z= 0.325 Chirality : 0.044 0.200 5834 Planarity : 0.005 0.062 6564 Dihedral : 14.926 146.577 6148 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 2.71 % Allowed : 11.24 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.13), residues: 4586 helix: 1.96 (0.09), residues: 2978 sheet: -0.32 (1.19), residues: 25 loop : -0.46 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 59 TYR 0.022 0.002 TYR w 129 PHE 0.029 0.002 PHE i 292 TRP 0.018 0.001 TRP u 86 HIS 0.008 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00488 (39673) covalent geometry : angle 0.64464 (53615) SS BOND : bond 0.00988 ( 6) SS BOND : angle 2.46014 ( 12) hydrogen bonds : bond 0.06183 ( 2317) hydrogen bonds : angle 4.31470 ( 6732) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 624 time to evaluate : 1.582 Fit side-chains revert: symmetry clash REVERT: S 4 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7390 (mm-30) REVERT: S 28 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8464 (mttt) REVERT: V 138 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: Y 102 ASP cc_start: 0.6050 (OUTLIER) cc_final: 0.5087 (m-30) REVERT: a 72 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8295 (ttm-80) REVERT: d 60 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8070 (tpm170) REVERT: e 151 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: h 6 VAL cc_start: 0.9311 (t) cc_final: 0.8947 (m) REVERT: i 48 PHE cc_start: 0.7636 (t80) cc_final: 0.7378 (t80) REVERT: i 251 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8658 (mtp) REVERT: j 16 LEU cc_start: 0.7905 (tt) cc_final: 0.7455 (tp) REVERT: j 17 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7906 (mp) REVERT: l 320 ASN cc_start: 0.8193 (t0) cc_final: 0.7871 (t0) REVERT: l 351 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8662 (m110) REVERT: l 493 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7765 (p) REVERT: l 496 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7524 (ttt) REVERT: m 57 PHE cc_start: 0.8674 (t80) cc_final: 0.8408 (t80) REVERT: n 46 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8291 (tmtt) REVERT: p 123 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: r 103 GLN cc_start: 0.9415 (OUTLIER) cc_final: 0.8874 (tt0) REVERT: s 258 ASN cc_start: 0.8744 (m-40) cc_final: 0.8425 (t0) REVERT: u 17 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7090 (mm-30) REVERT: v 29 TYR cc_start: 0.8054 (t80) cc_final: 0.7835 (t80) REVERT: v 39 MET cc_start: 0.8260 (tpt) cc_final: 0.7970 (tpt) REVERT: v 81 LYS cc_start: 0.8409 (mtpt) cc_final: 0.7551 (mtmt) REVERT: w 220 LYS cc_start: 0.7134 (mtmt) cc_final: 0.6795 (tptm) REVERT: w 227 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.6592 (mmm) REVERT: w 241 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7715 (t80) outliers start: 110 outliers final: 46 residues processed: 673 average time/residue: 0.8011 time to fit residues: 638.4706 Evaluate side-chains 671 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 608 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 102 ASP Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain h residue 54 LYS Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 251 MET Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 281 LEU Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain i residue 304 MET Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 267 MET Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 351 ASN Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 28 GLU Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 115 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 246 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 162 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 264 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 276 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 447 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 74 GLN Z 33 GLN c 164 ASN d 134 GLN e 145 ASN f 61 GLN g 14 GLN l 323 HIS ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 75 ASN r 304 GLN u 64 ASN v 47 ASN v 54 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.130764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.101322 restraints weight = 45452.505| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.35 r_work: 0.2863 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 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 = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 39680 Z= 0.127 Angle : 0.564 12.218 53627 Z= 0.283 Chirality : 0.040 0.253 5834 Planarity : 0.005 0.061 6564 Dihedral : 14.145 144.061 6146 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.47 % Favored : 96.49 % Rotamer: Outliers : 2.39 % Allowed : 12.27 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.13), residues: 4586 helix: 2.17 (0.09), residues: 2982 sheet: -0.22 (1.21), residues: 25 loop : -0.43 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 59 TYR 0.021 0.001 TYR r 406 PHE 0.028 0.001 PHE i 292 TRP 0.020 0.001 TRP l 144 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00275 (39673) covalent geometry : angle 0.56154 (53615) SS BOND : bond 0.01425 ( 6) SS BOND : angle 3.19736 ( 12) hydrogen bonds : bond 0.04980 ( 2317) hydrogen bonds : angle 4.14177 ( 6732) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 630 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: X 77 GLU cc_start: 0.8292 (tp30) cc_final: 0.7939 (tp30) REVERT: X 81 ASP cc_start: 0.8429 (m-30) cc_final: 0.8026 (m-30) REVERT: d 36 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8370 (mt) REVERT: d 60 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8210 (tpm170) REVERT: e 151 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: h 6 VAL cc_start: 0.9300 (t) cc_final: 0.8963 (m) REVERT: i 48 PHE cc_start: 0.7626 (t80) cc_final: 0.7349 (t80) REVERT: j 16 LEU cc_start: 0.7892 (tt) cc_final: 0.7463 (tp) REVERT: j 17 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7943 (mp) REVERT: j 90 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.9048 (mmm) REVERT: l 320 ASN cc_start: 0.8027 (t0) cc_final: 0.7694 (t0) REVERT: l 331 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.7956 (mmp) REVERT: l 405 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7958 (m-40) REVERT: l 493 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7710 (p) REVERT: l 496 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7505 (ttt) REVERT: l 525 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.7391 (mpt) REVERT: m 57 PHE cc_start: 0.8556 (t80) cc_final: 0.8322 (t80) REVERT: n 46 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8297 (tmtt) REVERT: p 123 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: p 144 THR cc_start: 0.8020 (t) cc_final: 0.7729 (m) REVERT: r 103 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.8743 (tt0) REVERT: s 25 ARG cc_start: 0.8654 (mtp180) cc_final: 0.8410 (mtp-110) REVERT: s 274 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8522 (ttt180) REVERT: u 17 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7038 (mm-30) REVERT: v 29 TYR cc_start: 0.8049 (t80) cc_final: 0.7812 (t80) REVERT: v 39 MET cc_start: 0.8193 (tpt) cc_final: 0.7922 (tpt) REVERT: v 81 LYS cc_start: 0.8393 (mtpt) cc_final: 0.7538 (mtmt) REVERT: w 220 LYS cc_start: 0.7102 (mtmt) cc_final: 0.6797 (tptm) REVERT: w 227 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.6533 (mmm) REVERT: w 241 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.7925 (t80) outliers start: 97 outliers final: 30 residues processed: 669 average time/residue: 0.7976 time to fit residues: 632.4827 Evaluate side-chains 662 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 615 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 331 MET Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 28 GLU Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 110 GLN Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 246 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 321 optimal weight: 0.0870 chunk 259 optimal weight: 2.9990 chunk 336 optimal weight: 3.9990 chunk 312 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 379 optimal weight: 3.9990 chunk 318 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 391 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 435 optimal weight: 0.0170 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 74 GLN Z 33 GLN c 164 ASN d 134 GLN e 145 ASN e 148 GLN f 61 GLN g 14 GLN l 56 HIS l 351 ASN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 304 GLN u 64 ASN v 47 ASN v 54 GLN ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.129381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.099795 restraints weight = 45680.117| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.27 r_work: 0.2889 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 39680 Z= 0.148 Angle : 0.587 13.172 53627 Z= 0.294 Chirality : 0.041 0.230 5834 Planarity : 0.005 0.060 6564 Dihedral : 13.824 143.023 6146 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 2.19 % Allowed : 12.84 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.13), residues: 4586 helix: 2.16 (0.09), residues: 2978 sheet: -0.16 (1.20), residues: 25 loop : -0.41 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 59 TYR 0.019 0.001 TYR r 406 PHE 0.029 0.002 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00342 (39673) covalent geometry : angle 0.58482 (53615) SS BOND : bond 0.01399 ( 6) SS BOND : angle 3.17097 ( 12) hydrogen bonds : bond 0.05271 ( 2317) hydrogen bonds : angle 4.14392 ( 6732) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 636 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: X 81 ASP cc_start: 0.8438 (m-30) cc_final: 0.8213 (m-30) REVERT: b 93 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8361 (mmtm) REVERT: d 36 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8416 (mt) REVERT: d 60 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8089 (tpm170) REVERT: e 69 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8502 (mtpt) REVERT: e 151 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: h 6 VAL cc_start: 0.9313 (t) cc_final: 0.9002 (m) REVERT: h 53 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8324 (tm-30) REVERT: i 48 PHE cc_start: 0.7646 (t80) cc_final: 0.7373 (t80) REVERT: j 16 LEU cc_start: 0.7961 (tt) cc_final: 0.7552 (tp) REVERT: j 17 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8023 (mp) REVERT: k 37 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8996 (ttp) REVERT: l 271 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8422 (tptt) REVERT: l 320 ASN cc_start: 0.8073 (t0) cc_final: 0.7754 (t0) REVERT: l 405 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7996 (m-40) REVERT: l 493 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7842 (p) REVERT: l 496 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7508 (ttt) REVERT: l 525 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.7430 (mpt) REVERT: l 562 LEU cc_start: 0.8104 (tt) cc_final: 0.7888 (tp) REVERT: m 57 PHE cc_start: 0.8541 (t80) cc_final: 0.8333 (t80) REVERT: n 46 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8282 (tmtt) REVERT: p 123 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: p 144 THR cc_start: 0.8070 (t) cc_final: 0.7776 (m) REVERT: r 103 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.8789 (tt0) REVERT: s 25 ARG cc_start: 0.8688 (mtp180) cc_final: 0.8446 (mtp-110) REVERT: s 258 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8404 (t0) REVERT: s 274 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8545 (ttt180) REVERT: u 17 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7099 (mm-30) REVERT: v 81 LYS cc_start: 0.8433 (mtpt) cc_final: 0.7631 (mtmt) REVERT: w 220 LYS cc_start: 0.7120 (mtmt) cc_final: 0.6818 (tptm) REVERT: w 227 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6569 (mmm) REVERT: w 241 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.8117 (t80) outliers start: 89 outliers final: 43 residues processed: 676 average time/residue: 0.8294 time to fit residues: 667.4711 Evaluate side-chains 679 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 615 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 54 LYS Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 281 LEU Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 37 MET Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 267 MET Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 110 GLN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 246 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 336 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 365 optimal weight: 4.9990 chunk 451 optimal weight: 0.4980 chunk 7 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 chunk 449 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 283 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 74 GLN Z 33 GLN c 164 ASN d 134 GLN d 149 HIS e 145 ASN e 148 GLN f 61 GLN l 351 ASN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 304 GLN u 64 ASN v 110 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.129118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.099171 restraints weight = 45695.442| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.35 r_work: 0.2844 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.081 | | 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) = 0.081 | | 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: 0.8863 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 39680 Z= 0.146 Angle : 0.584 12.130 53627 Z= 0.293 Chirality : 0.041 0.210 5834 Planarity : 0.005 0.060 6564 Dihedral : 13.575 143.921 6146 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 2.51 % Allowed : 13.35 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.13), residues: 4586 helix: 2.15 (0.09), residues: 2985 sheet: -0.13 (1.21), residues: 25 loop : -0.40 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 59 TYR 0.019 0.001 TYR r 406 PHE 0.029 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00339 (39673) covalent geometry : angle 0.58291 (53615) SS BOND : bond 0.01058 ( 6) SS BOND : angle 2.63942 ( 12) hydrogen bonds : bond 0.05244 ( 2317) hydrogen bonds : angle 4.13498 ( 6732) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 627 time to evaluate : 1.720 Fit side-chains revert: symmetry clash REVERT: U 39 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8431 (m) REVERT: X 77 GLU cc_start: 0.8339 (tp30) cc_final: 0.7955 (tp30) REVERT: X 81 ASP cc_start: 0.8462 (m-30) cc_final: 0.8052 (m-30) REVERT: b 93 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8391 (mmtm) REVERT: d 36 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8406 (mt) REVERT: d 60 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8127 (tpm170) REVERT: e 69 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8524 (mtpt) REVERT: e 151 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6640 (mp0) REVERT: h 6 VAL cc_start: 0.9306 (t) cc_final: 0.8987 (m) REVERT: h 53 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8383 (tm-30) REVERT: i 48 PHE cc_start: 0.7665 (t80) cc_final: 0.7360 (t80) REVERT: j 16 LEU cc_start: 0.7926 (tt) cc_final: 0.7516 (tp) REVERT: j 17 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7963 (mp) REVERT: l 271 LYS cc_start: 0.8800 (tppp) cc_final: 0.8426 (tptt) REVERT: l 320 ASN cc_start: 0.8090 (t0) cc_final: 0.7782 (t0) REVERT: l 405 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7981 (m-40) REVERT: l 493 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7807 (p) REVERT: l 496 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7505 (ttt) REVERT: l 525 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.7424 (mpt) REVERT: l 562 LEU cc_start: 0.8138 (tt) cc_final: 0.7924 (tp) REVERT: m 57 PHE cc_start: 0.8531 (t80) cc_final: 0.8321 (t80) REVERT: n 46 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8318 (tmtt) REVERT: p 123 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: p 144 THR cc_start: 0.8035 (t) cc_final: 0.7746 (m) REVERT: r 103 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.8776 (tt0) REVERT: r 448 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8757 (m) REVERT: s 25 ARG cc_start: 0.8698 (mtp180) cc_final: 0.8470 (mtp-110) REVERT: s 258 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8411 (t0) REVERT: s 274 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8525 (ttt180) REVERT: u 17 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7075 (mm-30) REVERT: v 29 TYR cc_start: 0.8031 (t80) cc_final: 0.7789 (t80) REVERT: v 81 LYS cc_start: 0.8408 (mtpt) cc_final: 0.7576 (mtmt) REVERT: w 175 ARG cc_start: 0.8282 (mtp85) cc_final: 0.7898 (mtt90) REVERT: w 176 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8140 (mp10) REVERT: w 220 LYS cc_start: 0.7128 (mtmt) cc_final: 0.6832 (tptm) REVERT: w 227 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.6518 (mmm) REVERT: w 241 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.8104 (t80) outliers start: 102 outliers final: 44 residues processed: 677 average time/residue: 0.8130 time to fit residues: 653.3562 Evaluate side-chains 684 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 618 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 54 LYS Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 281 LEU Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 28 GLU Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 115 LEU Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 176 GLN Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 246 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 321 optimal weight: 7.9990 chunk 280 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 216 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 337 optimal weight: 1.9990 chunk 365 optimal weight: 5.9990 chunk 218 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 74 GLN Z 33 GLN c 164 ASN d 134 GLN e 145 ASN e 148 GLN f 61 GLN r 304 GLN u 64 ASN v 54 GLN v 110 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.129018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.099323 restraints weight = 45589.911| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.29 r_work: 0.2850 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 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 = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 39680 Z= 0.151 Angle : 0.600 19.548 53627 Z= 0.300 Chirality : 0.042 0.277 5834 Planarity : 0.005 0.060 6564 Dihedral : 13.451 145.219 6146 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 2.43 % Allowed : 13.58 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.13), residues: 4586 helix: 2.14 (0.09), residues: 2983 sheet: -0.05 (1.21), residues: 25 loop : -0.40 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 59 TYR 0.019 0.001 TYR r 406 PHE 0.029 0.002 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00350 (39673) covalent geometry : angle 0.59904 (53615) SS BOND : bond 0.01205 ( 6) SS BOND : angle 2.60296 ( 12) hydrogen bonds : bond 0.05345 ( 2317) hydrogen bonds : angle 4.15345 ( 6732) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 625 time to evaluate : 1.598 Fit side-chains revert: symmetry clash REVERT: U 39 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8432 (m) REVERT: X 77 GLU cc_start: 0.8317 (tp30) cc_final: 0.7909 (tp30) REVERT: X 81 ASP cc_start: 0.8443 (m-30) cc_final: 0.8020 (m-30) REVERT: b 93 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8355 (mmtm) REVERT: c 36 MET cc_start: 0.8215 (mmp) cc_final: 0.7223 (mtp) REVERT: d 36 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8402 (mt) REVERT: d 60 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7991 (tpm170) REVERT: e 69 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8505 (mtpt) REVERT: e 151 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: h 6 VAL cc_start: 0.9303 (t) cc_final: 0.8990 (m) REVERT: h 53 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8304 (tm-30) REVERT: i 48 PHE cc_start: 0.7643 (t80) cc_final: 0.7374 (t80) REVERT: j 16 LEU cc_start: 0.7928 (tt) cc_final: 0.7532 (tp) REVERT: j 17 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7956 (mp) REVERT: k 37 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8947 (ttp) REVERT: l 60 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8534 (mt-10) REVERT: l 271 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8422 (tptt) REVERT: l 320 ASN cc_start: 0.8087 (t0) cc_final: 0.7773 (t0) REVERT: l 405 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7991 (m-40) REVERT: l 493 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7828 (p) REVERT: l 496 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7407 (ttt) REVERT: l 525 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.7430 (mpt) REVERT: l 562 LEU cc_start: 0.8184 (tt) cc_final: 0.7960 (tp) REVERT: m 57 PHE cc_start: 0.8519 (t80) cc_final: 0.8302 (t80) REVERT: n 46 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8287 (tmtt) REVERT: p 123 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: p 144 THR cc_start: 0.8043 (t) cc_final: 0.7745 (m) REVERT: r 103 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.8777 (tt0) REVERT: r 448 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8754 (m) REVERT: s 25 ARG cc_start: 0.8679 (mtp180) cc_final: 0.8446 (mtp-110) REVERT: s 258 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8403 (t0) REVERT: s 274 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8567 (ttt180) REVERT: u 17 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7057 (mm-30) REVERT: w 175 ARG cc_start: 0.8293 (mtp85) cc_final: 0.7913 (mtt90) REVERT: w 176 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8179 (mp10) REVERT: w 220 LYS cc_start: 0.7156 (mtmt) cc_final: 0.6846 (tptm) REVERT: w 227 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.6474 (mmm) REVERT: w 241 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7988 (t80) outliers start: 99 outliers final: 45 residues processed: 667 average time/residue: 0.8134 time to fit residues: 643.0882 Evaluate side-chains 688 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 619 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 54 LYS Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 49 ASN Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 281 LEU Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 37 MET Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 28 GLU Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 115 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 176 GLN Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 246 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 428 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 74 GLN Z 33 GLN c 164 ASN d 134 GLN e 145 ASN e 148 GLN f 61 GLN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 304 GLN u 64 ASN v 110 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 = 0.127919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.097847 restraints weight = 45608.909| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.33 r_work: 0.2827 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 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 = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 39680 Z= 0.170 Angle : 0.621 16.949 53627 Z= 0.310 Chirality : 0.043 0.331 5834 Planarity : 0.005 0.060 6564 Dihedral : 13.491 146.436 6146 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 2.26 % Allowed : 14.04 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.13), residues: 4586 helix: 2.12 (0.09), residues: 2975 sheet: -0.06 (1.21), residues: 25 loop : -0.43 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG v 56 TYR 0.019 0.002 TYR w 129 PHE 0.029 0.002 PHE i 292 TRP 0.018 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00405 (39673) covalent geometry : angle 0.61874 (53615) SS BOND : bond 0.01421 ( 6) SS BOND : angle 3.47824 ( 12) hydrogen bonds : bond 0.05595 ( 2317) hydrogen bonds : angle 4.18592 ( 6732) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 618 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: S 66 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7902 (mp) REVERT: U 39 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8441 (m) REVERT: X 77 GLU cc_start: 0.8337 (tp30) cc_final: 0.7942 (tp30) REVERT: X 81 ASP cc_start: 0.8466 (m-30) cc_final: 0.8052 (m-30) REVERT: c 36 MET cc_start: 0.8209 (mmp) cc_final: 0.7235 (mtt) REVERT: d 36 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8418 (mt) REVERT: d 60 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8025 (tpm170) REVERT: e 69 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8519 (mtpt) REVERT: e 151 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: h 6 VAL cc_start: 0.9315 (t) cc_final: 0.8994 (m) REVERT: h 53 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: i 48 PHE cc_start: 0.7678 (t80) cc_final: 0.7404 (t80) REVERT: j 16 LEU cc_start: 0.7956 (tt) cc_final: 0.7540 (tp) REVERT: j 17 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7959 (mp) REVERT: k 37 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8978 (ttp) REVERT: l 140 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8941 (tt) REVERT: l 271 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8434 (tptt) REVERT: l 320 ASN cc_start: 0.8159 (t0) cc_final: 0.7835 (t0) REVERT: l 405 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.8063 (m-40) REVERT: l 493 VAL cc_start: 0.8175 (OUTLIER) cc_final: 0.7850 (p) REVERT: l 496 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7429 (ttt) REVERT: l 525 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.7478 (mpt) REVERT: l 562 LEU cc_start: 0.8207 (tt) cc_final: 0.7988 (tp) REVERT: m 57 PHE cc_start: 0.8565 (t80) cc_final: 0.8341 (t80) REVERT: n 46 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8310 (tmtt) REVERT: p 123 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: p 144 THR cc_start: 0.8075 (t) cc_final: 0.7755 (m) REVERT: r 103 GLN cc_start: 0.9366 (OUTLIER) cc_final: 0.8788 (tt0) REVERT: r 448 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8745 (m) REVERT: s 25 ARG cc_start: 0.8701 (mtp180) cc_final: 0.8467 (mtp-110) REVERT: s 258 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8451 (t0) REVERT: s 274 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8547 (ttt180) REVERT: u 17 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7096 (mm-30) REVERT: v 29 TYR cc_start: 0.7968 (t80) cc_final: 0.7741 (t80) REVERT: w 175 ARG cc_start: 0.8300 (mtp85) cc_final: 0.7918 (mtt90) REVERT: w 176 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8174 (mp10) REVERT: w 220 LYS cc_start: 0.7152 (mtmt) cc_final: 0.6855 (tptm) REVERT: w 227 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.6484 (mmm) REVERT: w 241 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8020 (t80) outliers start: 92 outliers final: 47 residues processed: 664 average time/residue: 0.8079 time to fit residues: 637.3926 Evaluate side-chains 683 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 611 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 54 LYS Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 281 LEU Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain i residue 304 MET Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 37 MET Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 28 GLU Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 115 LEU Chi-restraints excluded: chain v residue 43 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 176 GLN Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 354 optimal weight: 0.8980 chunk 325 optimal weight: 7.9990 chunk 375 optimal weight: 0.9980 chunk 315 optimal weight: 4.9990 chunk 219 optimal weight: 0.9990 chunk 327 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 251 optimal weight: 4.9990 chunk 90 optimal weight: 0.1980 chunk 340 optimal weight: 4.9990 chunk 312 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 74 GLN Z 33 GLN b 89 HIS c 164 ASN d 134 GLN e 148 GLN f 61 GLN r 304 GLN u 64 ASN u 65 GLN v 54 GLN v 110 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.132425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.103533 restraints weight = 45634.015| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.29 r_work: 0.2893 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.107 39680 Z= 0.117 Angle : 0.559 15.257 53627 Z= 0.279 Chirality : 0.040 0.294 5834 Planarity : 0.005 0.060 6564 Dihedral : 12.911 146.030 6146 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 1.62 % Allowed : 14.83 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.13), residues: 4586 helix: 2.28 (0.09), residues: 2985 sheet: 0.06 (1.19), residues: 25 loop : -0.37 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 59 TYR 0.023 0.001 TYR l 422 PHE 0.028 0.001 PHE i 292 TRP 0.025 0.001 TRP l 144 HIS 0.006 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00248 (39673) covalent geometry : angle 0.55653 (53615) SS BOND : bond 0.01321 ( 6) SS BOND : angle 3.26139 ( 12) hydrogen bonds : bond 0.04489 ( 2317) hydrogen bonds : angle 4.03617 ( 6732) Misc. bond : bond 0.00015 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 631 time to evaluate : 1.509 Fit side-chains revert: symmetry clash REVERT: X 77 GLU cc_start: 0.8321 (tp30) cc_final: 0.7887 (tp30) REVERT: X 81 ASP cc_start: 0.8435 (m-30) cc_final: 0.8055 (m-30) REVERT: c 36 MET cc_start: 0.8191 (mmp) cc_final: 0.7211 (mtt) REVERT: d 60 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8010 (tpm170) REVERT: h 6 VAL cc_start: 0.9294 (t) cc_final: 0.8969 (m) REVERT: h 53 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8305 (tm-30) REVERT: i 48 PHE cc_start: 0.7653 (t80) cc_final: 0.7366 (t80) REVERT: j 16 LEU cc_start: 0.7907 (tt) cc_final: 0.7508 (tp) REVERT: j 17 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7892 (mp) REVERT: j 72 LEU cc_start: 0.8588 (mt) cc_final: 0.8373 (mm) REVERT: k 37 MET cc_start: 0.9164 (tmt) cc_final: 0.8958 (ttp) REVERT: l 271 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8386 (tptt) REVERT: l 320 ASN cc_start: 0.7846 (t0) cc_final: 0.7610 (t0) REVERT: l 493 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7715 (p) REVERT: l 496 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7398 (ttt) REVERT: l 562 LEU cc_start: 0.8105 (tt) cc_final: 0.7870 (tp) REVERT: n 46 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8273 (tmtt) REVERT: p 123 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: p 135 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6880 (ttm110) REVERT: r 103 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.8658 (tt0) REVERT: s 25 ARG cc_start: 0.8688 (mtp180) cc_final: 0.8468 (mtp-110) REVERT: s 258 ASN cc_start: 0.8670 (m-40) cc_final: 0.8341 (t0) REVERT: s 274 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8469 (ttt180) REVERT: u 17 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.6954 (mm-30) REVERT: u 139 GLU cc_start: 0.6984 (pm20) cc_final: 0.6424 (pp20) REVERT: v 29 TYR cc_start: 0.7964 (t80) cc_final: 0.7680 (t80) REVERT: v 81 LYS cc_start: 0.8393 (mtpt) cc_final: 0.7478 (mtmt) REVERT: w 175 ARG cc_start: 0.8285 (mtp85) cc_final: 0.7951 (mtt90) REVERT: w 176 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8160 (mp10) REVERT: w 220 LYS cc_start: 0.7114 (mtmt) cc_final: 0.6822 (tptm) REVERT: w 227 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7208 (mmm) REVERT: w 241 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.7988 (t80) outliers start: 66 outliers final: 32 residues processed: 668 average time/residue: 0.8029 time to fit residues: 636.6146 Evaluate side-chains 659 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 612 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 54 LYS Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 281 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 28 GLU Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 176 GLN Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 275 optimal weight: 7.9990 chunk 452 optimal weight: 5.9990 chunk 408 optimal weight: 0.7980 chunk 425 optimal weight: 0.0770 chunk 360 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 451 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 214 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 74 GLN Z 33 GLN d 134 GLN e 145 ASN e 148 GLN f 61 GLN v 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.132670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.103379 restraints weight = 45732.587| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.30 r_work: 0.2907 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 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 = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 39680 Z= 0.119 Angle : 0.568 15.586 53627 Z= 0.283 Chirality : 0.040 0.292 5834 Planarity : 0.005 0.061 6564 Dihedral : 12.765 145.529 6146 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 1.50 % Allowed : 15.22 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.13), residues: 4586 helix: 2.33 (0.09), residues: 2985 sheet: 0.18 (1.19), residues: 25 loop : -0.34 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 59 TYR 0.022 0.001 TYR l 422 PHE 0.028 0.001 PHE i 292 TRP 0.021 0.001 TRP l 144 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00259 (39673) covalent geometry : angle 0.56580 (53615) SS BOND : bond 0.01344 ( 6) SS BOND : angle 3.23863 ( 12) hydrogen bonds : bond 0.04492 ( 2317) hydrogen bonds : angle 4.01771 ( 6732) Misc. bond : bond 0.00020 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17767.54 seconds wall clock time: 301 minutes 59.16 seconds (18119.16 seconds total)