Starting phenix.real_space_refine on Mon Jul 6 23:45:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vbl_31881/07_2026/7vbl_31881.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbl_31881/07_2026/7vbl_31881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vbl_31881/07_2026/7vbl_31881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbl_31881/07_2026/7vbl_31881.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vbl_31881/07_2026/7vbl_31881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbl_31881/07_2026/7vbl_31881.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vbl_31881/07_2026/7vbl_31881.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vbl_31881/07_2026/7vbl_31881.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 293 5.16 5 C 26117 2.51 5 N 6281 2.21 5 O 7413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40142 Number of models: 1 Model: "" Number of chains: 63 Chain: "Q" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 7, 'TRANS': 36} Chain: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 691 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 611 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 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: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1005 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} 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: 4797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4797 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 577} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "m" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1273 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 45 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: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2590 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "U" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 194 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "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: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 134 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "j" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "l" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 231 Unusual residues: {'CDL': 1, 'PEE': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "m" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 354 Unusual residues: {'CDL': 2, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "s" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 127 Unusual residues: {' UQ': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 25 Chain: "u" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "S" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "j" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "k" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "l" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "m" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "n" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Chain: "s" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "w" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.50 Time building chain proxies: 6.40, per 1000 atoms: 0.16 Number of scatterers: 40142 At special positions: 0 Unit cell: (183.151, 190.133, 136.423, 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 293 16.00 P 38 15.00 O 7413 8.00 N 6281 7.00 C 26117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.04 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.04 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.21 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.02 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.7 seconds 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8956 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 5 sheets defined 70.6% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'Q' and resid 40 through 45 Processing helix chain 'Q' and resid 46 through 48 No H-bonds generated for 'chain 'Q' and resid 46 through 48' Processing helix chain 'Q' and resid 57 through 61 removed outlier: 3.654A pdb=" N HIS Q 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 1 through 4 Processing helix chain 'S' and resid 5 through 30 removed outlier: 3.661A pdb=" N ILE S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 41 through 56 removed outlier: 4.284A pdb=" N GLY S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 removed outlier: 3.526A pdb=" N ILE S 69 " --> pdb=" O LEU S 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 16 Processing helix chain 'U' and resid 16 through 32 Processing helix chain 'U' and resid 33 through 36 removed outlier: 3.676A pdb=" N SER U 36 " --> pdb=" O PRO U 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 33 through 36' Processing helix chain 'U' and resid 38 through 48 Processing helix chain 'U' and resid 78 through 83 Processing helix chain 'V' and resid 3 through 11 Processing helix chain 'V' and resid 17 through 44 Processing helix chain 'V' and resid 48 through 81 Processing helix chain 'V' and resid 86 through 106 removed outlier: 4.241A pdb=" N TYR V 90 " --> pdb=" O ASP V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 132 Processing helix chain 'W' and resid 33 through 98 Proline residue: W 73 - end of helix Processing helix chain 'W' and resid 120 through 126 Processing helix chain 'W' and resid 129 through 143 removed outlier: 5.856A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.298A 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 removed outlier: 3.502A pdb=" N LEU X 98 " --> pdb=" O PRO X 95 " (cutoff:3.500A) 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: 3.781A 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 removed outlier: 3.538A pdb=" N GLN Z 21 " --> pdb=" O ASP Z 18 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP Z 22 " --> pdb=" O TYR Z 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 18 through 22' Processing helix chain 'Z' and resid 27 through 38 removed outlier: 3.725A pdb=" N THR Z 31 " --> pdb=" O THR Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 50 removed outlier: 3.644A pdb=" N GLU Z 49 " --> pdb=" O TRP Z 45 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 55 removed outlier: 4.320A pdb=" N GLY Z 55 " --> 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 89 removed outlier: 3.602A pdb=" N GLU Z 89 " --> pdb=" O GLU Z 85 " (cutoff:3.500A) 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: 3.596A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE a 113 " --> pdb=" O TRP a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 115 through 126 removed outlier: 3.520A pdb=" N TYR a 126 " --> pdb=" O ALA a 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 128 through 164 removed outlier: 4.099A pdb=" N ASN a 132 " --> pdb=" O GLY a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 179 Processing helix chain 'b' and resid 5 through 26 Processing helix chain 'b' and resid 69 through 74 removed outlier: 3.582A pdb=" N THR b 73 " --> pdb=" O ILE b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 89 Processing helix chain 'b' and resid 90 through 93 Processing helix chain 'c' and resid 33 through 37 removed outlier: 3.599A pdb=" N PHE c 37 " --> pdb=" O LYS c 34 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 55 Processing helix chain 'c' and resid 108 through 112 Processing helix chain 'c' and resid 128 through 150 Processing helix chain 'd' and resid 28 through 59 removed outlier: 3.557A pdb=" N TYR d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix removed outlier: 3.547A pdb=" N LYS d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN d 59 " --> pdb=" O GLN d 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 77 removed outlier: 3.513A pdb=" N CYS d 77 " --> pdb=" O ILE d 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 117 Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'd' and resid 125 through 144 Processing helix chain 'd' and resid 151 through 175 Processing helix chain 'e' and resid 65 through 70 removed outlier: 4.243A pdb=" N LYS e 69 " --> pdb=" O ASN e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 96 Processing helix chain 'e' and resid 97 through 108 Processing helix chain 'e' and resid 114 through 132 Processing helix chain 'f' and resid 40 through 74 Processing helix chain 'g' and resid 17 through 23 Processing helix chain 'g' and resid 30 through 51 Processing helix chain 'g' and resid 59 through 99 removed outlier: 3.759A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 103 Processing helix chain 'h' and resid 5 through 11 Processing helix chain 'h' and resid 15 through 19 Processing helix chain 'h' and resid 25 through 29 Processing helix chain 'h' and resid 33 through 45 Processing helix chain 'h' and resid 48 through 56 removed outlier: 4.124A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 56 through 69 Processing helix chain 'h' and resid 69 through 89 removed outlier: 3.527A pdb=" N GLU h 89 " --> pdb=" O LYS h 85 " (cutoff:3.500A) Processing helix chain 'h' and resid 95 through 99 Processing helix chain 'i' and resid 2 through 23 Processing helix chain 'i' and resid 25 through 45 Proline residue: i 42 - end of helix removed outlier: 3.620A pdb=" N MET i 45 " --> pdb=" O ILE i 41 " (cutoff:3.500A) 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: 4.170A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 123 through 133 Processing helix chain 'i' and resid 135 through 145 Processing helix chain 'i' and resid 150 through 170 Processing helix chain 'i' and resid 174 through 193 removed outlier: 3.785A pdb=" N VAL i 193 " --> pdb=" O TRP i 189 " (cutoff:3.500A) Processing helix chain 'i' and resid 197 through 222 removed outlier: 3.532A 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: 3.541A pdb=" N THR i 241 " --> pdb=" O MET i 237 " (cutoff:3.500A) Processing helix chain 'i' and resid 259 through 273 removed outlier: 4.346A pdb=" N LYS i 263 " --> pdb=" O GLY i 259 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN i 273 " --> pdb=" O GLU i 269 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 301 removed outlier: 4.729A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 315 removed outlier: 3.789A 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 347 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 24 Processing helix chain 'j' and resid 30 through 35 Processing helix chain 'j' and resid 55 through 73 removed outlier: 3.553A pdb=" N LEU j 63 " --> pdb=" O ALA j 59 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU j 64 " --> pdb=" O ILE j 60 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 79 Processing helix chain 'j' and resid 83 through 108 Processing helix chain 'k' and resid 2 through 21 removed outlier: 3.525A pdb=" N MET k 6 " --> pdb=" O PRO k 2 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 52 removed outlier: 4.043A pdb=" N SER k 29 " --> pdb=" O HIS k 25 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 57 Processing helix chain 'k' and resid 58 through 86 Processing helix chain 'k' and resid 89 through 93 removed outlier: 3.544A pdb=" N ASN k 92 " --> pdb=" O TYR k 89 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 14 removed outlier: 4.364A pdb=" N SER l 6 " --> pdb=" O ASN l 2 " (cutoff:3.500A) removed outlier: 3.815A 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 29 removed outlier: 6.096A pdb=" N ASN l 25 " --> pdb=" O SER l 22 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE l 26 " --> pdb=" O ASN l 23 " (cutoff:3.500A) Processing helix chain 'l' and resid 31 through 58 removed outlier: 4.422A 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: 3.881A 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 193 removed outlier: 3.902A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 197 through 205 Processing helix chain 'l' and resid 209 through 224 removed outlier: 4.229A pdb=" N LEU l 213 " --> pdb=" O PRO l 209 " (cutoff:3.500A) Processing helix chain 'l' and resid 231 through 236 removed outlier: 3.593A pdb=" N SER l 235 " --> pdb=" O PRO l 231 " (cutoff:3.500A) 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 251 through 253 No H-bonds generated for 'chain 'l' and resid 251 through 253' Processing helix chain 'l' and resid 254 through 263 Processing helix chain 'l' and resid 263 through 268 Processing helix chain 'l' and resid 270 through 293 removed outlier: 3.541A pdb=" N GLN l 274 " --> pdb=" O ASN l 270 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) Processing helix chain 'l' and resid 297 through 319 Processing helix chain 'l' and resid 321 through 350 removed outlier: 4.004A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (cutoff:3.500A) Processing helix chain 'l' and resid 355 through 359 Processing helix chain 'l' and resid 366 through 381 Processing helix chain 'l' and resid 386 through 401 removed outlier: 3.690A pdb=" N TYR l 390 " --> pdb=" O LEU l 386 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER l 391 " --> pdb=" O THR l 387 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE l 395 " --> pdb=" O SER l 391 " (cutoff:3.500A) Processing helix chain 'l' and resid 405 through 432 removed outlier: 3.765A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU l 432 " --> pdb=" O PHE l 428 " (cutoff:3.500A) Processing helix chain 'l' and resid 447 through 471 removed outlier: 5.715A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.408A 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 Processing helix chain 'l' and resid 517 through 525 Processing helix chain 'l' and resid 528 through 534 Processing helix chain 'l' and resid 535 through 548 Processing helix chain 'l' and resid 556 through 562 removed outlier: 3.708A pdb=" N LEU l 562 " --> pdb=" O LEU l 558 " (cutoff:3.500A) Processing helix chain 'l' and resid 562 through 579 Processing helix chain 'l' and resid 583 through 602 removed outlier: 3.535A pdb=" N THR l 600 " --> pdb=" O MET l 596 " (cutoff:3.500A) Processing helix chain 'm' and resid 4 through 22 Processing helix chain 'm' and resid 25 through 46 Processing helix chain 'm' and resid 49 through 75 Processing helix chain 'm' and resid 86 through 110 removed outlier: 3.762A pdb=" N GLU m 110 " --> pdb=" O TYR m 106 " (cutoff:3.500A) Processing helix chain 'm' and resid 123 through 128 removed outlier: 3.764A pdb=" N VAL m 126 " --> pdb=" O GLY m 123 " (cutoff:3.500A) Processing helix chain 'm' and resid 137 through 145 Processing helix chain 'm' and resid 150 through 172 Processing helix chain 'n' and resid 4 through 12 Processing helix chain 'n' and resid 15 through 33 Processing helix chain 'o' and resid 15 through 24 Proline residue: o 20 - end of helix removed outlier: 3.558A pdb=" N ASP o 24 " --> pdb=" O ALA o 21 " (cutoff:3.500A) Processing helix chain 'o' and resid 26 through 52 removed outlier: 3.701A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) 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 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 11 through 31 Processing helix chain 'p' and resid 33 through 50 Processing helix chain 'p' and resid 56 through 75 Processing helix chain 'p' and resid 94 through 98 Processing helix chain 'p' and resid 100 through 107 removed outlier: 3.505A pdb=" N TRP p 107 " --> pdb=" O LEU p 104 " (cutoff:3.500A) Processing helix chain 'p' and resid 108 through 114 removed outlier: 3.879A pdb=" N MET p 114 " --> pdb=" O SER p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 115 through 143 removed outlier: 3.703A pdb=" N PHE p 119 " --> pdb=" O TYR p 115 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (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: 3.859A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 22 through 39 Processing helix chain 'r' and resid 40 through 43 removed outlier: 3.938A pdb=" N ASN r 43 " --> pdb=" O SER r 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 40 through 43' Processing helix chain 'r' and resid 61 through 81 removed outlier: 4.113A pdb=" N LEU r 65 " --> pdb=" O LEU r 61 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 88 through 112 removed outlier: 3.515A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 114 through 125 Processing helix chain 'r' and resid 125 through 137 removed outlier: 3.700A pdb=" N THR r 129 " --> pdb=" O THR r 125 " (cutoff:3.500A) Processing helix chain 'r' and resid 141 through 172 removed outlier: 3.656A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY r 156 " --> pdb=" O TYR r 152 " (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: 4.939A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 223 removed outlier: 4.086A 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: 4.015A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 258 Processing helix chain 'r' and resid 258 through 278 removed outlier: 3.710A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG r 278 " --> pdb=" O SER r 274 " (cutoff:3.500A) Processing helix chain 'r' and resid 281 through 304 removed outlier: 3.546A pdb=" N ILE r 286 " --> pdb=" O LEU r 282 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN r 304 " --> pdb=" O ALA r 300 " (cutoff:3.500A) Processing helix chain 'r' and resid 305 through 338 removed outlier: 3.683A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 347 through 352 removed outlier: 4.107A 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: 4.209A pdb=" N LEU r 395 " --> pdb=" O ILE r 391 " (cutoff:3.500A) Processing helix chain 'r' and resid 430 through 450 Proline residue: r 443 - end of helix removed outlier: 3.654A pdb=" N THR r 448 " --> pdb=" O LEU r 444 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU r 449 " --> pdb=" O LEU r 445 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN r 450 " --> pdb=" O LEU r 446 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 456 removed outlier: 4.194A pdb=" N GLY r 456 " --> 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: 3.726A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 45 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 124 removed outlier: 3.711A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN s 124 " --> pdb=" O GLY s 120 " (cutoff:3.500A) Processing helix chain 's' and resid 125 through 155 removed outlier: 5.102A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 169 removed outlier: 4.077A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 193 Proline residue: s 180 - end of helix Processing helix chain 's' and resid 203 through 208 Processing helix chain 's' and resid 209 through 213 removed outlier: 3.559A pdb=" N VAL s 213 " --> pdb=" O GLY s 210 " (cutoff:3.500A) Processing helix chain 's' and resid 216 through 243 removed outlier: 3.672A pdb=" N PHE s 220 " --> pdb=" O ALA s 216 " (cutoff:3.500A) Processing helix chain 's' and resid 251 through 277 removed outlier: 4.300A pdb=" N TYR s 255 " --> pdb=" O THR s 251 " (cutoff:3.500A) Processing helix chain 's' and resid 281 through 292 removed outlier: 3.519A pdb=" N MET s 286 " --> pdb=" O TYR s 282 " (cutoff:3.500A) Processing helix chain 's' and resid 292 through 311 removed outlier: 3.639A pdb=" N LEU s 296 " --> pdb=" O SER s 292 " (cutoff:3.500A) Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 21 through 36 removed outlier: 4.961A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 36 through 51 removed outlier: 3.515A 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 removed outlier: 3.554A pdb=" N GLY u 60 " --> pdb=" O CYS u 56 " (cutoff:3.500A) Processing helix chain 'u' and resid 78 through 92 removed outlier: 3.898A pdb=" N PHE u 82 " --> pdb=" O CYS u 78 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER u 92 " --> pdb=" O CYS u 88 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 115 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 12 through 16 Processing helix chain 'v' and resid 42 through 50 Processing helix chain 'v' and resid 59 through 73 removed outlier: 3.521A pdb=" N LEU v 63 " --> pdb=" O CYS v 59 " (cutoff:3.500A) Processing helix chain 'v' and resid 80 through 124 removed outlier: 3.645A pdb=" N GLN v 84 " --> pdb=" O CYS v 80 " (cutoff:3.500A) Processing helix chain 'w' and resid 39 through 45 Processing helix chain 'w' and resid 69 through 82 Processing helix chain 'w' and resid 92 through 98 removed outlier: 3.728A pdb=" N THR w 97 " --> pdb=" O TYR w 93 " (cutoff:3.500A) 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: 3.905A pdb=" N LEU w 170 " --> pdb=" O ASP w 166 " (cutoff:3.500A) Processing helix chain 'w' and resid 180 through 195 Processing helix chain 'w' and resid 196 through 198 No H-bonds generated for 'chain 'w' and resid 196 through 198' Processing helix chain 'w' and resid 210 through 222 removed outlier: 3.746A pdb=" N GLY w 222 " --> pdb=" O ILE w 218 " (cutoff:3.500A) Processing helix chain 'w' and resid 225 through 229 Processing helix chain 'w' and resid 230 through 250 removed outlier: 3.679A pdb=" N LEU w 234 " --> pdb=" O THR w 230 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix Processing helix chain 'w' and resid 261 through 264 removed outlier: 3.720A pdb=" N GLU w 264 " --> pdb=" O ARG w 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 261 through 264' Processing helix chain 'w' and resid 265 through 275 removed outlier: 3.544A pdb=" N TYR w 275 " --> pdb=" O GLU w 271 " (cutoff:3.500A) Processing helix chain 'w' and resid 282 through 286 Processing helix chain 'w' and resid 287 through 299 removed outlier: 3.631A pdb=" N GLN w 299 " --> pdb=" O ARG w 295 " (cutoff:3.500A) Processing helix chain 'w' and resid 300 through 306 Processing helix chain 'w' and resid 307 through 310 removed outlier: 3.853A pdb=" N ILE w 310 " --> pdb=" O TYR w 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 307 through 310' Processing helix chain 'w' and resid 320 through 332 Processing helix chain 'w' and resid 340 through 348 removed outlier: 3.976A pdb=" N ASN w 344 " --> pdb=" O PRO w 341 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU w 345 " --> pdb=" O GLY w 342 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASP w 346 " --> pdb=" O TYR w 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'U' and resid 57 through 58 removed outlier: 6.327A pdb=" N LEU U 57 " --> pdb=" O VAL u 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'a' and resid 97 through 98 removed outlier: 5.925A pdb=" N GLU a 97 " --> pdb=" O TYR d 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'b' and resid 97 through 99 removed outlier: 7.599A pdb=" N ASN l 65 " --> pdb=" O PHE l 80 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N PHE l 80 " --> pdb=" O ASN l 65 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS l 67 " --> pdb=" O LEU l 78 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU l 78 " --> pdb=" O HIS l 67 " (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 'w' and resid 84 through 85 removed outlier: 6.706A pdb=" N ARG w 84 " --> pdb=" O VAL w 158 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE w 60 " --> pdb=" O LEU w 159 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR w 61 " --> pdb=" O VAL w 205 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL w 207 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP w 63 " --> pdb=" O VAL w 207 " (cutoff:3.500A) 2314 hydrogen bonds defined for protein. 6738 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: 6.84 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 6033 1.32 - 1.46: 13563 1.46 - 1.60: 20512 1.60 - 1.74: 75 1.74 - 1.88: 530 Bond restraints: 40713 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.297 0.227 2.00e-02 2.50e+03 1.29e+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 u 201 " pdb=" OA8 CDL u 201 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" CB7 CDL a 201 " pdb=" OB8 CDL a 201 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 bond pdb=" CA7 CDL l 702 " pdb=" OA8 CDL l 702 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.15e+02 ... (remaining 40708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 53888 3.44 - 6.89: 846 6.89 - 10.33: 133 10.33 - 13.77: 28 13.77 - 17.22: 13 Bond angle restraints: 54908 Sorted by residual: angle pdb=" N ILE s 10 " pdb=" CA ILE s 10 " pdb=" C ILE s 10 " ideal model delta sigma weight residual 110.72 122.90 -12.18 1.01e+00 9.80e-01 1.45e+02 angle pdb=" N ILE r 441 " pdb=" CA ILE r 441 " pdb=" C ILE r 441 " ideal model delta sigma weight residual 110.62 121.36 -10.74 1.02e+00 9.61e-01 1.11e+02 angle pdb=" N ILE r 5 " pdb=" CA ILE r 5 " pdb=" C ILE r 5 " ideal model delta sigma weight residual 110.72 121.20 -10.48 1.01e+00 9.80e-01 1.08e+02 angle pdb=" C ALA X 71 " pdb=" N PRO X 72 " pdb=" CA PRO X 72 " ideal model delta sigma weight residual 119.66 126.72 -7.06 7.20e-01 1.93e+00 9.63e+01 angle pdb=" N ILE i 277 " pdb=" CA ILE i 277 " pdb=" C ILE i 277 " ideal model delta sigma weight residual 110.62 120.06 -9.44 1.02e+00 9.61e-01 8.56e+01 ... (remaining 54903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 23776 35.72 - 71.44: 780 71.44 - 107.16: 50 107.16 - 142.87: 18 142.87 - 178.59: 8 Dihedral angle restraints: 24632 sinusoidal: 10773 harmonic: 13859 Sorted by residual: dihedral pdb=" CA LYS b 121 " pdb=" C LYS b 121 " pdb=" N GLU b 122 " pdb=" CA GLU b 122 " ideal model delta harmonic sigma weight residual 180.00 146.27 33.73 0 5.00e+00 4.00e-02 4.55e+01 dihedral pdb=" CB CYS u 78 " pdb=" SG CYS u 78 " pdb=" SG CYS u 110 " pdb=" CB CYS u 110 " ideal model delta sinusoidal sigma weight residual -86.00 -144.05 58.05 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 77.17 -137.16 1 2.00e+01 2.50e-03 4.16e+01 ... (remaining 24629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 5642 0.120 - 0.239: 250 0.239 - 0.359: 29 0.359 - 0.478: 8 0.478 - 0.598: 4 Chirality restraints: 5933 Sorted by residual: chirality pdb=" CA TYR s 282 " pdb=" N TYR s 282 " pdb=" C TYR s 282 " pdb=" CB TYR s 282 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.93e+00 chirality pdb=" CA PHE r 151 " pdb=" N PHE r 151 " pdb=" C PHE r 151 " pdb=" CB PHE r 151 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" CA HIS r 422 " pdb=" N HIS r 422 " pdb=" C HIS r 422 " pdb=" CB HIS r 422 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.03e+00 ... (remaining 5930 not shown) Planarity restraints: 6671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " 0.358 2.00e-02 2.50e+03 3.29e-01 1.36e+03 pdb=" C18 UQ s 402 " -0.349 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " -0.389 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " 0.004 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " 0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 402 " -0.056 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C11 UQ s 402 " 0.037 2.00e-02 2.50e+03 pdb=" C7 UQ s 402 " -0.290 2.00e-02 2.50e+03 pdb=" C8 UQ s 402 " 0.549 2.00e-02 2.50e+03 pdb=" C9 UQ s 402 " -0.240 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 402 " -0.110 2.00e-02 2.50e+03 1.82e-01 4.14e+02 pdb=" C13 UQ s 402 " 0.034 2.00e-02 2.50e+03 pdb=" C14 UQ s 402 " 0.334 2.00e-02 2.50e+03 pdb=" C15 UQ s 402 " -0.067 2.00e-02 2.50e+03 pdb=" C16 UQ s 402 " -0.191 2.00e-02 2.50e+03 ... (remaining 6668 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 110 2.35 - 2.98: 20116 2.98 - 3.62: 60606 3.62 - 4.26: 101176 4.26 - 4.90: 162525 Nonbonded interactions: 344533 Sorted by model distance: nonbonded pdb=" OE2 GLU a 97 " pdb=" CD ARG d 60 " model vdw 1.707 3.440 nonbonded pdb=" OE2 GLU m 77 " pdb=" O HOH m 301 " model vdw 1.996 3.040 nonbonded pdb=" O TYR l 27 " pdb=" ND2 ASN l 115 " model vdw 2.046 3.120 nonbonded pdb=" OE2 GLU i 269 " pdb=" O HOH i 501 " model vdw 2.074 3.040 nonbonded pdb=" O PRO j 36 " pdb=" O HOH j 301 " model vdw 2.081 3.040 ... (remaining 344528 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.360 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.370 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 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 : 0.011 0.882 40724 Z= 0.731 Angle : 1.093 17.216 54924 Z= 0.634 Chirality : 0.063 0.598 5933 Planarity : 0.008 0.329 6671 Dihedral : 17.280 178.593 15652 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Rotamer: Outliers : 0.98 % Allowed : 3.22 % Favored : 95.81 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.12), residues: 4667 helix: 0.49 (0.09), residues: 2962 sheet: -2.04 (0.86), residues: 25 loop : -1.08 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG W 68 TYR 0.026 0.002 TYR m 4 PHE 0.042 0.002 PHE s 270 TRP 0.021 0.002 TRP u 86 HIS 0.018 0.002 HIS l 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00966 / 0.52 (40713) covalent geometry : angle 1.09169 / 0.63 (54908) SS BOND : bond 0.06218 / 4.78 ( 8) SS BOND : angle 2.97545 / 1.78 ( 16) hydrogen bonds : bond 0.14899 / 9.95 ( 2314) hydrogen bonds : angle 5.54651 / 3.93 ( 6738) Misc. bond : bond 0.60124 / 26.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 893 time to evaluate : 1.279 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 56 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7491 (mmmt) REVERT: U 16 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7372 (mm-30) REVERT: U 38 TYR cc_start: 0.7669 (m-80) cc_final: 0.7426 (m-80) REVERT: V 140 LYS cc_start: 0.8027 (tttt) cc_final: 0.7517 (mmtm) REVERT: Y 90 SER cc_start: 0.8360 (m) cc_final: 0.7976 (p) REVERT: a 95 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7871 (mt-10) REVERT: c 36 MET cc_start: 0.7349 (mmp) cc_final: 0.6793 (mtt) REVERT: f 70 LYS cc_start: 0.8480 (mttt) cc_final: 0.8192 (mttm) REVERT: h 71 LYS cc_start: 0.8764 (mttt) cc_final: 0.8503 (mttm) REVERT: i 14 MET cc_start: 0.8907 (mtp) cc_final: 0.8636 (mtp) REVERT: i 34 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8283 (mm-30) REVERT: i 69 MET cc_start: 0.8556 (mtp) cc_final: 0.8318 (mtp) REVERT: i 202 ILE cc_start: 0.9046 (mt) cc_final: 0.8841 (mm) REVERT: i 321 LYS cc_start: 0.7376 (tppt) cc_final: 0.7156 (mmmm) REVERT: n 31 SER cc_start: 0.8558 (t) cc_final: 0.8352 (m) REVERT: o 31 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7889 (ttpp) REVERT: o 111 LYS cc_start: 0.8133 (mttt) cc_final: 0.7869 (mttp) REVERT: p 13 GLN cc_start: 0.7642 (tm-30) cc_final: 0.6729 (mp10) REVERT: p 65 ARG cc_start: 0.7323 (ttt90) cc_final: 0.7097 (mtp-110) REVERT: p 66 GLN cc_start: 0.7383 (mt0) cc_final: 0.7172 (mt0) REVERT: p 124 GLN cc_start: 0.7977 (mt0) cc_final: 0.7680 (mt0) REVERT: r 22 MET cc_start: 0.8825 (mmm) cc_final: 0.8594 (mmp) REVERT: r 78 MET cc_start: 0.9107 (mtt) cc_final: 0.8888 (mtp) REVERT: r 401 MET cc_start: 0.8247 (ttp) cc_final: 0.7678 (tpp) REVERT: w 293 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7507 (ttp80) outliers start: 40 outliers final: 7 residues processed: 909 average time/residue: 0.8024 time to fit residues: 860.9349 Evaluate side-chains 679 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 671 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 155 TYR Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain d residue 62 TYR Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 140 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 38 GLN S 27 HIS S 61 HIS U 11 ASN V 129 GLN W 61 GLN W 85 GLN Y 39 HIS Y 54 GLN Y 57 GLN a 132 ASN b 83 HIS c 84 GLN c 160 GLN c 183 HIS d 56 HIS d 91 GLN d 107 GLN d 159 GLN e 74 HIS e 86 ASN f 61 GLN g 18 ASN g 99 HIS h 21 GLN i 47 ASN i 83 GLN i 91 ASN i 172 GLN i 174 GLN i 273 ASN j 28 ASN k 92 ASN l 2 ASN l 165 ASN l 226 GLN l 230 HIS l 446 ASN l 524 ASN ** l 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 46 ASN p 26 HIS p 108 HIS p 139 GLN p 141 GLN r 43 ASN r 51 ASN r 83 HIS r 139 GLN r 399 ASN r 421 HIS r 440 HIS s 5 ASN s 171 HIS s 230 ASN s 287 HIS u 16 GLN v 61 HIS v 92 HIS w 107 GLN w 127 ASN w 142 GLN w 176 GLN w 186 HIS w 235 GLN w 239 ASN w 286 GLN w 292 HIS w 323 GLN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.126828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.102985 restraints weight = 43450.184| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.02 r_work: 0.2927 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40724 Z= 0.137 Angle : 0.607 12.910 54924 Z= 0.309 Chirality : 0.041 0.184 5933 Planarity : 0.005 0.050 6671 Dihedral : 16.553 179.788 6465 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 2.15 % Allowed : 9.12 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.12), residues: 4667 helix: 1.63 (0.09), residues: 3000 sheet: -1.60 (0.87), residues: 25 loop : -0.66 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG w 51 TYR 0.027 0.001 TYR r 406 PHE 0.031 0.001 PHE i 292 TRP 0.021 0.001 TRP u 86 HIS 0.007 0.001 HIS l 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (40713) covalent geometry : angle 0.60664 / 0.31 (54908) SS BOND : bond 0.00474 / 0.27 ( 8) SS BOND : angle 1.91189 / 1.03 ( 16) hydrogen bonds : bond 0.05563 / 3.78 ( 2314) hydrogen bonds : angle 4.39400 / 3.15 ( 6738) Misc. bond : bond 0.00094 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 714 time to evaluate : 1.410 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 16 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7510 (mm-30) REVERT: U 71 GLN cc_start: 0.8365 (mt0) cc_final: 0.8048 (mt0) REVERT: V 8 LYS cc_start: 0.7861 (mtmt) cc_final: 0.6737 (tmtt) REVERT: V 120 LEU cc_start: 0.8720 (tp) cc_final: 0.8277 (mt) REVERT: W 52 LYS cc_start: 0.8224 (mtmt) cc_final: 0.8021 (ttpt) REVERT: W 93 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7481 (tp30) REVERT: X 151 LYS cc_start: 0.8872 (tppp) cc_final: 0.8474 (tptm) REVERT: Y 90 SER cc_start: 0.8311 (m) cc_final: 0.7968 (p) REVERT: Z 30 GLU cc_start: 0.8008 (tp30) cc_final: 0.7679 (tp30) REVERT: a 72 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8403 (ttm170) REVERT: c 36 MET cc_start: 0.8116 (mmp) cc_final: 0.7388 (mtt) REVERT: d 78 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: e 54 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.5275 (mmt90) REVERT: h 53 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8513 (tt0) REVERT: i 69 MET cc_start: 0.9156 (mtp) cc_final: 0.8924 (mtp) REVERT: i 278 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8228 (tpt) REVERT: i 321 LYS cc_start: 0.7668 (tppt) cc_final: 0.7361 (mmmm) REVERT: j 16 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8303 (mp) REVERT: j 19 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8269 (mm) REVERT: k 1 MET cc_start: 0.6885 (mtp) cc_final: 0.6406 (ttp) REVERT: k 10 MET cc_start: 0.9086 (tpt) cc_final: 0.8820 (tpt) REVERT: l 55 MET cc_start: 0.9098 (mtp) cc_final: 0.8893 (mtt) REVERT: l 496 MET cc_start: 0.8219 (mtp) cc_final: 0.7657 (tmm) REVERT: o 31 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8662 (ttpp) REVERT: o 111 LYS cc_start: 0.8349 (mttt) cc_final: 0.8097 (mttp) REVERT: p 13 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7499 (mp10) REVERT: p 59 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7600 (tttp) REVERT: r 22 MET cc_start: 0.9037 (mmm) cc_final: 0.8828 (mmp) REVERT: r 398 MET cc_start: 0.8693 (mtp) cc_final: 0.8470 (mtm) REVERT: s 258 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8322 (t0) REVERT: u 19 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7483 (ptpt) REVERT: u 76 ARG cc_start: 0.7324 (ttm110) cc_final: 0.7076 (ttp80) REVERT: u 80 GLU cc_start: 0.6624 (tp30) cc_final: 0.5721 (tp30) REVERT: u 84 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: w 51 ARG cc_start: 0.7692 (ptp-110) cc_final: 0.6765 (ttp-110) REVERT: w 72 ARG cc_start: 0.7785 (ttp-170) cc_final: 0.7559 (ttt180) REVERT: w 264 GLU cc_start: 0.7642 (mp0) cc_final: 0.7404 (mp0) outliers start: 88 outliers final: 23 residues processed: 747 average time/residue: 0.8105 time to fit residues: 716.3329 Evaluate side-chains 700 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 665 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 44 LYS Chi-restraints excluded: chain W residue 93 GLU Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain e residue 54 ARG Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 115 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain u residue 19 LYS Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain v residue 70 LYS Chi-restraints excluded: chain v residue 94 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 169 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 134 optimal weight: 0.0570 chunk 250 optimal weight: 0.0170 chunk 416 optimal weight: 1.9990 chunk 408 optimal weight: 6.9990 chunk 272 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 11 ASN W 85 GLN W 90 ASN e 65 ASN e 145 ASN f 61 GLN f 73 ASN i 36 ASN i 134 GLN l 34 ASN ** l 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 46 ASN p 141 GLN r 139 GLN u 64 ASN w 37 GLN w 239 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.126600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.102800 restraints weight = 43446.374| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.02 r_work: 0.2926 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 40724 Z= 0.121 Angle : 0.547 9.742 54924 Z= 0.280 Chirality : 0.040 0.189 5933 Planarity : 0.004 0.043 6671 Dihedral : 15.138 178.537 6453 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 2.15 % Allowed : 11.17 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.12), residues: 4667 helix: 2.09 (0.09), residues: 2997 sheet: -0.96 (0.86), residues: 25 loop : -0.39 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG p 65 TYR 0.022 0.001 TYR r 406 PHE 0.032 0.001 PHE i 292 TRP 0.021 0.001 TRP u 86 HIS 0.007 0.001 HIS l 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (40713) covalent geometry : angle 0.54627 / 0.28 (54908) SS BOND : bond 0.00292 / 0.20 ( 8) SS BOND : angle 1.51910 / 0.94 ( 16) hydrogen bonds : bond 0.05063 / 3.45 ( 2314) hydrogen bonds : angle 4.16444 / 2.98 ( 6738) Misc. bond : bond 0.00069 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 709 time to evaluate : 1.692 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: Q 56 LYS cc_start: 0.8128 (pttt) cc_final: 0.7896 (pttt) REVERT: U 16 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7505 (mm-30) REVERT: U 71 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8155 (mt0) REVERT: V 120 LEU cc_start: 0.8755 (tp) cc_final: 0.8300 (mt) REVERT: W 52 LYS cc_start: 0.8244 (mtmt) cc_final: 0.8016 (ttpt) REVERT: W 93 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7557 (tp30) REVERT: Y 90 SER cc_start: 0.8411 (m) cc_final: 0.8044 (p) REVERT: Z 49 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7511 (mm-30) REVERT: a 72 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8261 (ttm170) REVERT: a 106 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8507 (t) REVERT: b 35 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8297 (mt) REVERT: c 36 MET cc_start: 0.7987 (mmp) cc_final: 0.7281 (mtt) REVERT: c 85 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8573 (mt-10) REVERT: e 54 ARG cc_start: 0.6290 (OUTLIER) cc_final: 0.5361 (mmt90) REVERT: h 53 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: i 40 MET cc_start: 0.9215 (tpt) cc_final: 0.8929 (mmm) REVERT: i 69 MET cc_start: 0.9160 (mtp) cc_final: 0.8934 (mtp) REVERT: i 278 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8184 (tpt) REVERT: i 321 LYS cc_start: 0.7750 (tppt) cc_final: 0.7402 (mmmm) REVERT: j 16 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8174 (mm) REVERT: j 19 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8254 (mm) REVERT: k 1 MET cc_start: 0.7210 (mtp) cc_final: 0.6939 (ttp) REVERT: l 53 MET cc_start: 0.9086 (mtt) cc_final: 0.8885 (mtp) REVERT: o 111 LYS cc_start: 0.8330 (mttt) cc_final: 0.8088 (mttp) REVERT: p 13 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7559 (mp10) REVERT: p 66 GLN cc_start: 0.8355 (mt0) cc_final: 0.8056 (mp10) REVERT: r 22 MET cc_start: 0.8990 (mmm) cc_final: 0.8790 (mmp) REVERT: r 47 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6917 (mm-30) REVERT: r 114 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: r 398 MET cc_start: 0.8675 (mtp) cc_final: 0.8445 (mtm) REVERT: s 103 LEU cc_start: 0.8495 (tp) cc_final: 0.8253 (mt) REVERT: s 143 GLU cc_start: 0.8613 (tp30) cc_final: 0.8339 (tm-30) REVERT: s 253 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7379 (pm20) REVERT: u 6 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6898 (tm-30) REVERT: u 76 ARG cc_start: 0.7328 (ttm110) cc_final: 0.7104 (ttp80) REVERT: u 109 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.6234 (tm-30) REVERT: v 86 ASP cc_start: 0.8609 (m-30) cc_final: 0.8406 (m-30) REVERT: v 115 ARG cc_start: 0.7553 (ttp-110) cc_final: 0.7130 (mtp-110) REVERT: w 72 ARG cc_start: 0.7862 (ttp-170) cc_final: 0.7461 (ttp80) REVERT: w 251 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7340 (mt-10) outliers start: 88 outliers final: 26 residues processed: 745 average time/residue: 0.8175 time to fit residues: 719.9609 Evaluate side-chains 700 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 657 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 44 LYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 93 GLU Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 54 ARG Chi-restraints excluded: chain e residue 138 GLU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain i residue 157 MET Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain s residue 253 GLU Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain w residue 251 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 145 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 344 optimal weight: 7.9990 chunk 417 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 336 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 296 optimal weight: 4.9990 chunk 440 optimal weight: 4.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 11 ASN W 85 GLN e 65 ASN e 145 ASN f 61 GLN l 34 ASN ** l 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 46 ASN o 79 ASN p 141 GLN r 139 GLN r 304 GLN u 104 GLN w 107 GLN w 132 GLN w 202 HIS w 239 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.123590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.101643 restraints weight = 43348.099| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.00 r_work: 0.2876 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9090 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40724 Z= 0.138 Angle : 0.575 10.965 54924 Z= 0.291 Chirality : 0.041 0.195 5933 Planarity : 0.004 0.044 6671 Dihedral : 14.690 179.417 6453 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 2.56 % Allowed : 11.48 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.12), residues: 4667 helix: 2.15 (0.09), residues: 3004 sheet: -0.81 (0.90), residues: 25 loop : -0.28 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d 43 TYR 0.025 0.002 TYR d 32 PHE 0.030 0.002 PHE i 292 TRP 0.021 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (40713) covalent geometry : angle 0.57419 / 0.29 (54908) SS BOND : bond 0.00327 / 0.22 ( 8) SS BOND : angle 1.36994 / 0.87 ( 16) hydrogen bonds : bond 0.05478 / 3.73 ( 2314) hydrogen bonds : angle 4.15854 / 2.98 ( 6738) Misc. bond : bond 0.00053 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 675 time to evaluate : 1.557 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 48 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8589 (mtm) REVERT: U 71 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8235 (mt0) REVERT: V 8 LYS cc_start: 0.7847 (mtmt) cc_final: 0.6930 (tmtt) REVERT: V 120 LEU cc_start: 0.8812 (tp) cc_final: 0.8370 (mt) REVERT: W 52 LYS cc_start: 0.8325 (mtmt) cc_final: 0.7971 (ttpp) REVERT: W 93 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7599 (tp30) REVERT: X 151 LYS cc_start: 0.8931 (tppp) cc_final: 0.8627 (tptm) REVERT: Y 90 SER cc_start: 0.8476 (m) cc_final: 0.8134 (p) REVERT: Z 61 VAL cc_start: 0.8652 (m) cc_final: 0.8309 (p) REVERT: a 72 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8336 (ttm170) REVERT: a 106 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8606 (t) REVERT: c 36 MET cc_start: 0.8030 (mmp) cc_final: 0.7406 (mtt) REVERT: c 85 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8587 (mt-10) REVERT: e 54 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5336 (mmt90) REVERT: h 53 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: i 69 MET cc_start: 0.9179 (mtp) cc_final: 0.8940 (mtp) REVERT: i 278 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8280 (tpt) REVERT: i 321 LYS cc_start: 0.7780 (tppt) cc_final: 0.7485 (mmmm) REVERT: j 16 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8245 (mm) REVERT: j 19 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8270 (mm) REVERT: l 59 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: m 5 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7949 (mt) REVERT: n 41 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8750 (mttt) REVERT: o 111 LYS cc_start: 0.8350 (mttt) cc_final: 0.8133 (mttp) REVERT: p 13 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7574 (mp10) REVERT: p 59 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8183 (tttp) REVERT: p 65 ARG cc_start: 0.8444 (mtp180) cc_final: 0.7938 (mtp-110) REVERT: p 66 GLN cc_start: 0.8432 (mt0) cc_final: 0.8082 (mp10) REVERT: p 150 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7584 (mmt180) REVERT: r 47 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6906 (mm-30) REVERT: r 114 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: s 103 LEU cc_start: 0.8538 (tp) cc_final: 0.8325 (mt) REVERT: u 6 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: u 76 ARG cc_start: 0.7405 (ttm110) cc_final: 0.7189 (ttp80) REVERT: u 80 GLU cc_start: 0.6717 (tp30) cc_final: 0.5753 (tp30) REVERT: u 84 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: v 115 ARG cc_start: 0.7665 (ttp-110) cc_final: 0.7253 (mtp-110) REVERT: w 251 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7332 (mt-10) outliers start: 105 outliers final: 41 residues processed: 720 average time/residue: 0.7971 time to fit residues: 678.5921 Evaluate side-chains 716 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 655 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain S residue 48 MET Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 44 LYS Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 93 GLU Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 54 ARG Chi-restraints excluded: chain e residue 138 GLU Chi-restraints excluded: chain g residue 92 MET Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain i residue 157 MET Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 38 GLU Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 150 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 62 SER Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain s residue 125 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain w residue 251 GLU Chi-restraints excluded: chain w residue 254 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 375 optimal weight: 6.9990 chunk 227 optimal weight: 7.9990 chunk 422 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 415 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 443 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 319 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 31 ASN U 11 ASN U 71 GLN W 90 ASN c 160 GLN e 145 ASN f 61 GLN l 34 ASN l 579 ASN m 46 ASN n 3 ASN p 124 GLN p 141 GLN p 169 HIS r 139 GLN r 304 GLN v 4 HIS w 239 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.096377 restraints weight = 42859.872| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.02 r_work: 0.2775 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 40724 Z= 0.259 Angle : 0.727 15.219 54924 Z= 0.371 Chirality : 0.049 0.236 5933 Planarity : 0.006 0.064 6671 Dihedral : 15.240 179.734 6453 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.60 % Favored : 96.29 % Rotamer: Outliers : 3.12 % Allowed : 11.29 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.59 (0.12), residues: 4667 helix: 1.83 (0.09), residues: 2996 sheet: -0.93 (0.92), residues: 25 loop : -0.33 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG d 43 TYR 0.028 0.002 TYR w 129 PHE 0.028 0.003 PHE i 292 TRP 0.022 0.002 TRP u 86 HIS 0.014 0.002 HIS l 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.26 (40713) covalent geometry : angle 0.72620 / 0.37 (54908) SS BOND : bond 0.00559 / 0.37 ( 8) SS BOND : angle 2.33591 / 1.34 ( 16) hydrogen bonds : bond 0.07620 / 5.17 ( 2314) hydrogen bonds : angle 4.47146 / 3.20 ( 6738) Misc. bond : bond 0.00091 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 654 time to evaluate : 1.396 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 4 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: V 8 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7028 (tmtt) REVERT: V 120 LEU cc_start: 0.8841 (tp) cc_final: 0.8409 (mt) REVERT: W 52 LYS cc_start: 0.8408 (mtmt) cc_final: 0.8062 (ttpp) REVERT: W 93 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7761 (tp30) REVERT: Y 90 SER cc_start: 0.8529 (m) cc_final: 0.8192 (p) REVERT: Z 61 VAL cc_start: 0.8733 (m) cc_final: 0.8322 (p) REVERT: a 72 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8378 (ttm170) REVERT: c 36 MET cc_start: 0.8084 (mmp) cc_final: 0.7479 (mtt) REVERT: c 85 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8684 (mt-10) REVERT: e 54 ARG cc_start: 0.6213 (OUTLIER) cc_final: 0.5348 (mmt90) REVERT: e 145 ASN cc_start: 0.8650 (m110) cc_final: 0.8366 (m110) REVERT: g 51 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8089 (mpt180) REVERT: h 53 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8605 (tt0) REVERT: i 69 MET cc_start: 0.9228 (mtp) cc_final: 0.9028 (mtp) REVERT: i 278 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8537 (tpt) REVERT: i 321 LYS cc_start: 0.8007 (tppt) cc_final: 0.7628 (mmmm) REVERT: j 1 MET cc_start: 0.7560 (tmt) cc_final: 0.7078 (tpt) REVERT: k 10 MET cc_start: 0.9152 (tpt) cc_final: 0.8872 (tpt) REVERT: l 59 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: o 22 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: o 111 LYS cc_start: 0.8406 (mttt) cc_final: 0.8153 (mttp) REVERT: p 13 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8177 (tm-30) REVERT: p 59 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8375 (tttp) REVERT: p 65 ARG cc_start: 0.8494 (mtp180) cc_final: 0.7989 (mtp-110) REVERT: p 66 GLN cc_start: 0.8495 (mt0) cc_final: 0.8153 (mp10) REVERT: p 150 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8175 (mmt180) REVERT: r 1 MET cc_start: 0.8913 (tpt) cc_final: 0.8684 (tpt) REVERT: r 59 ASP cc_start: 0.8075 (t0) cc_final: 0.7734 (t70) REVERT: r 454 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.8726 (pp) REVERT: s 227 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: s 251 THR cc_start: 0.8409 (m) cc_final: 0.7969 (t) REVERT: u 6 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6959 (tm-30) REVERT: u 76 ARG cc_start: 0.7469 (ttm110) cc_final: 0.7235 (ttp80) REVERT: u 109 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6314 (tt0) REVERT: v 115 ARG cc_start: 0.7780 (ttp-110) cc_final: 0.7572 (mtp-110) REVERT: w 72 ARG cc_start: 0.7790 (ttt180) cc_final: 0.7551 (ttp80) REVERT: w 171 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8336 (tp30) REVERT: w 262 GLU cc_start: 0.8276 (pt0) cc_final: 0.8066 (pt0) REVERT: w 330 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8678 (ttmt) REVERT: w 354 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8760 (mp) outliers start: 128 outliers final: 48 residues processed: 714 average time/residue: 0.8105 time to fit residues: 683.2040 Evaluate side-chains 703 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 636 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain V residue 44 LYS Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 93 GLU Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 54 ARG Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 138 GLU Chi-restraints excluded: chain g residue 51 ARG Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 73 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 38 GLU Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 316 THR Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain o residue 22 GLU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 150 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 62 SER Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 125 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain v residue 34 ARG Chi-restraints excluded: chain w residue 171 GLU Chi-restraints excluded: chain w residue 254 GLU Chi-restraints excluded: chain w residue 330 LYS Chi-restraints excluded: chain w residue 354 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 293 optimal weight: 0.0270 chunk 202 optimal weight: 7.9990 chunk 369 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 379 optimal weight: 4.9990 chunk 307 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 326 optimal weight: 3.9990 chunk 452 optimal weight: 5.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 11 ASN W 85 GLN Z 60 ASN f 61 GLN p 53 ASN p 141 GLN r 139 GLN r 304 GLN u 104 GLN v 65 GLN w 239 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.121231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.098948 restraints weight = 43373.631| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.02 r_work: 0.2831 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40724 Z= 0.149 Angle : 0.596 11.818 54924 Z= 0.304 Chirality : 0.042 0.198 5933 Planarity : 0.005 0.054 6671 Dihedral : 14.610 173.945 6453 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 2.78 % Allowed : 12.12 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.12), residues: 4667 helix: 2.07 (0.09), residues: 3006 sheet: -0.89 (0.90), residues: 25 loop : -0.25 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG w 51 TYR 0.021 0.002 TYR w 129 PHE 0.031 0.002 PHE i 292 TRP 0.020 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (40713) covalent geometry : angle 0.59386 / 0.30 (54908) SS BOND : bond 0.00348 / 0.24 ( 8) SS BOND : angle 2.80037 / 1.50 ( 16) hydrogen bonds : bond 0.05928 / 4.03 ( 2314) hydrogen bonds : angle 4.26704 / 3.06 ( 6738) Misc. bond : bond 0.00059 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 658 time to evaluate : 1.068 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 4 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8436 (mp0) REVERT: V 8 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7020 (tmtt) REVERT: V 120 LEU cc_start: 0.8830 (tp) cc_final: 0.8385 (mt) REVERT: W 52 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8031 (ttpp) REVERT: X 105 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8202 (mpp) REVERT: X 151 LYS cc_start: 0.9009 (tppp) cc_final: 0.8652 (tptm) REVERT: Y 90 SER cc_start: 0.8552 (m) cc_final: 0.8226 (p) REVERT: Z 61 VAL cc_start: 0.8643 (m) cc_final: 0.8290 (p) REVERT: a 72 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8333 (ttm170) REVERT: c 36 MET cc_start: 0.8042 (mmp) cc_final: 0.7466 (mtt) REVERT: c 85 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8663 (mt-10) REVERT: d 168 LYS cc_start: 0.7997 (tmmt) cc_final: 0.7632 (ttmm) REVERT: e 54 ARG cc_start: 0.6104 (OUTLIER) cc_final: 0.5251 (mmt90) REVERT: e 116 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: e 145 ASN cc_start: 0.8640 (m110) cc_final: 0.8374 (m110) REVERT: h 37 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: h 53 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8588 (tt0) REVERT: i 69 MET cc_start: 0.9214 (mtp) cc_final: 0.8981 (mtp) REVERT: i 278 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8385 (tpt) REVERT: i 321 LYS cc_start: 0.8003 (tppt) cc_final: 0.7613 (mmmm) REVERT: j 1 MET cc_start: 0.7444 (tmt) cc_final: 0.7013 (tpt) REVERT: j 19 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8283 (mm) REVERT: k 10 MET cc_start: 0.9101 (tpt) cc_final: 0.8809 (tpt) REVERT: o 111 LYS cc_start: 0.8385 (mttt) cc_final: 0.8136 (mttp) REVERT: p 65 ARG cc_start: 0.8467 (mtp180) cc_final: 0.7944 (mtp-110) REVERT: p 66 GLN cc_start: 0.8483 (mt0) cc_final: 0.8160 (mp10) REVERT: p 150 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7513 (mmt180) REVERT: r 45 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7663 (mt) REVERT: r 114 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: s 103 LEU cc_start: 0.8577 (tp) cc_final: 0.8364 (mt) REVERT: s 200 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8582 (mm) REVERT: s 227 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: s 251 THR cc_start: 0.8252 (m) cc_final: 0.7879 (t) REVERT: s 258 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8435 (t0) REVERT: u 6 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.6960 (tm-30) REVERT: u 11 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7587 (tp30) REVERT: u 84 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: u 109 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6316 (tt0) REVERT: v 115 ARG cc_start: 0.7802 (ttp-110) cc_final: 0.7525 (mtp-110) REVERT: w 72 ARG cc_start: 0.7705 (ttt180) cc_final: 0.7375 (ttp80) outliers start: 114 outliers final: 38 residues processed: 709 average time/residue: 0.7999 time to fit residues: 671.1425 Evaluate side-chains 697 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 640 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain V residue 44 LYS Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 54 ARG Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 138 GLU Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 38 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 491 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 69 GLU Chi-restraints excluded: chain p residue 150 ARG Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 62 SER Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain s residue 125 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain v residue 94 ASP Chi-restraints excluded: chain w residue 254 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 16 optimal weight: 5.9990 chunk 438 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 362 optimal weight: 10.0000 chunk 402 optimal weight: 1.9990 chunk 190 optimal weight: 0.0030 chunk 246 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 chunk 443 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 11 ASN W 85 GLN W 90 ASN f 61 GLN p 13 GLN p 53 ASN p 124 GLN p 141 GLN r 139 GLN r 304 GLN w 107 GLN w 239 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.096897 restraints weight = 43362.523| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 0.99 r_work: 0.2804 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 40724 Z= 0.183 Angle : 0.637 13.283 54924 Z= 0.324 Chirality : 0.044 0.222 5933 Planarity : 0.005 0.053 6671 Dihedral : 14.405 170.027 6453 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.54 % Favored : 96.36 % Rotamer: Outliers : 2.51 % Allowed : 12.63 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.12), residues: 4667 helix: 2.02 (0.09), residues: 3012 sheet: -1.04 (0.91), residues: 23 loop : -0.25 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG w 51 TYR 0.025 0.002 TYR w 129 PHE 0.029 0.002 PHE i 292 TRP 0.024 0.002 TRP u 86 HIS 0.008 0.001 HIS r 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (40713) covalent geometry : angle 0.63567 / 0.32 (54908) SS BOND : bond 0.00433 / 0.29 ( 8) SS BOND : angle 2.37741 / 1.44 ( 16) hydrogen bonds : bond 0.06498 / 4.41 ( 2314) hydrogen bonds : angle 4.32004 / 3.09 ( 6738) Misc. bond : bond 0.00081 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 649 time to evaluate : 1.585 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 4 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: V 6 LEU cc_start: 0.8113 (mt) cc_final: 0.7371 (tp) REVERT: V 8 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7101 (tmtt) REVERT: V 120 LEU cc_start: 0.8847 (tp) cc_final: 0.8417 (mt) REVERT: W 52 LYS cc_start: 0.8415 (mtmt) cc_final: 0.8063 (ttpp) REVERT: Y 90 SER cc_start: 0.8561 (m) cc_final: 0.8259 (p) REVERT: Z 61 VAL cc_start: 0.8652 (m) cc_final: 0.8289 (p) REVERT: a 72 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8348 (ttm170) REVERT: b 35 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8331 (mt) REVERT: c 85 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8664 (mt-10) REVERT: d 168 LYS cc_start: 0.8034 (tmmt) cc_final: 0.7683 (ttmm) REVERT: e 54 ARG cc_start: 0.6220 (OUTLIER) cc_final: 0.5347 (mmt90) REVERT: e 116 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: g 51 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8075 (mpt180) REVERT: g 97 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8763 (ttmt) REVERT: h 37 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: h 53 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: i 69 MET cc_start: 0.9221 (mtp) cc_final: 0.9002 (mtp) REVERT: i 278 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8443 (tpt) REVERT: i 321 LYS cc_start: 0.8053 (tppt) cc_final: 0.7633 (mmmm) REVERT: i 324 LYS cc_start: 0.8256 (tptt) cc_final: 0.8011 (tptt) REVERT: k 10 MET cc_start: 0.9111 (tpt) cc_final: 0.8829 (tpt) REVERT: o 111 LYS cc_start: 0.8426 (mttt) cc_final: 0.8182 (mttp) REVERT: p 65 ARG cc_start: 0.8474 (mtp180) cc_final: 0.7974 (mtp-110) REVERT: p 66 GLN cc_start: 0.8512 (mt0) cc_final: 0.8187 (mp10) REVERT: p 150 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7580 (mmt180) REVERT: r 45 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7756 (mt) REVERT: r 59 ASP cc_start: 0.7985 (t0) cc_final: 0.7635 (t70) REVERT: r 114 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: r 454 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.8696 (pp) REVERT: s 200 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8530 (mm) REVERT: s 227 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: s 251 THR cc_start: 0.8295 (m) cc_final: 0.7833 (t) REVERT: s 253 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7856 (pm20) REVERT: s 258 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8479 (t0) REVERT: u 6 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: u 11 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7576 (tp30) REVERT: u 84 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: u 109 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6334 (tt0) REVERT: v 115 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7597 (mtp-110) REVERT: w 72 ARG cc_start: 0.7754 (ttt180) cc_final: 0.7538 (ttp80) REVERT: w 171 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8307 (tp30) REVERT: w 226 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7361 (mt-10) REVERT: w 261 ARG cc_start: 0.7242 (tmm-80) cc_final: 0.6877 (tmm-80) REVERT: w 330 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8683 (ttmt) outliers start: 103 outliers final: 45 residues processed: 692 average time/residue: 0.8409 time to fit residues: 686.1549 Evaluate side-chains 713 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 644 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain V residue 44 LYS Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain c residue 68 ASP Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 54 ARG Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 138 GLU Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 51 ARG Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 38 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 316 THR Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 13 GLN Chi-restraints excluded: chain p residue 69 GLU Chi-restraints excluded: chain p residue 150 ARG Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 62 SER Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 125 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 253 GLU Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain w residue 171 GLU Chi-restraints excluded: chain w residue 254 GLU Chi-restraints excluded: chain w residue 330 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 91 optimal weight: 0.4980 chunk 300 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 438 optimal weight: 0.5980 chunk 332 optimal weight: 0.8980 chunk 294 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 329 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 11 ASN W 85 GLN e 145 ASN f 61 GLN l 175 ASN p 53 ASN p 141 GLN r 139 GLN w 239 ASN w 322 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.124346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.102307 restraints weight = 43486.478| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.04 r_work: 0.2895 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 40724 Z= 0.116 Angle : 0.540 9.951 54924 Z= 0.275 Chirality : 0.039 0.182 5933 Planarity : 0.004 0.049 6671 Dihedral : 13.663 162.790 6453 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.85 % Favored : 97.06 % Rotamer: Outliers : 1.66 % Allowed : 13.75 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 2.13 (0.12), residues: 4667 helix: 2.25 (0.09), residues: 3022 sheet: -0.86 (0.88), residues: 23 loop : -0.15 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG w 51 TYR 0.024 0.001 TYR l 422 PHE 0.032 0.001 PHE i 292 TRP 0.024 0.001 TRP l 144 HIS 0.009 0.001 HIS p 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (40713) covalent geometry : angle 0.53938 / 0.27 (54908) SS BOND : bond 0.00323 / 0.22 ( 8) SS BOND : angle 1.64777 / 0.99 ( 16) hydrogen bonds : bond 0.04854 / 3.30 ( 2314) hydrogen bonds : angle 4.10328 / 2.94 ( 6738) Misc. bond : bond 0.00027 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 673 time to evaluate : 1.567 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: S 4 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: V 8 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7631 (ttmm) REVERT: V 120 LEU cc_start: 0.8819 (tp) cc_final: 0.8392 (mt) REVERT: X 151 LYS cc_start: 0.9000 (tppp) cc_final: 0.8656 (tptm) REVERT: Y 90 SER cc_start: 0.8546 (m) cc_final: 0.8260 (p) REVERT: Z 61 VAL cc_start: 0.8590 (m) cc_final: 0.8239 (p) REVERT: a 72 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8277 (ttm170) REVERT: c 85 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8646 (mt-10) REVERT: d 101 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8859 (mm-30) REVERT: d 168 LYS cc_start: 0.8002 (tmmt) cc_final: 0.7651 (ttmm) REVERT: e 54 ARG cc_start: 0.6137 (OUTLIER) cc_final: 0.5236 (mmt90) REVERT: h 37 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8364 (tt0) REVERT: h 53 GLU cc_start: 0.8792 (tt0) cc_final: 0.8522 (tt0) REVERT: i 69 MET cc_start: 0.9178 (mtp) cc_final: 0.8941 (mtp) REVERT: i 278 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8159 (tpt) REVERT: i 321 LYS cc_start: 0.8021 (tppt) cc_final: 0.7619 (mmmm) REVERT: i 324 LYS cc_start: 0.8165 (tptt) cc_final: 0.7914 (tptt) REVERT: l 387 THR cc_start: 0.9010 (t) cc_final: 0.8643 (m) REVERT: l 581 LYS cc_start: 0.8639 (mttt) cc_final: 0.8353 (mtmt) REVERT: o 111 LYS cc_start: 0.8348 (mttt) cc_final: 0.8135 (mttp) REVERT: p 13 GLN cc_start: 0.8192 (tt0) cc_final: 0.7741 (mp10) REVERT: p 65 ARG cc_start: 0.8416 (mtp180) cc_final: 0.7933 (mtp-110) REVERT: p 66 GLN cc_start: 0.8479 (mt0) cc_final: 0.8183 (mp10) REVERT: p 150 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8151 (mmt180) REVERT: r 45 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7543 (mt) REVERT: s 227 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: s 251 THR cc_start: 0.8217 (m) cc_final: 0.7804 (t) REVERT: s 253 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: u 6 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: u 11 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7643 (tp30) REVERT: u 84 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: u 109 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6305 (tt0) REVERT: v 15 LYS cc_start: 0.8236 (mtpp) cc_final: 0.8033 (mtpm) REVERT: v 115 ARG cc_start: 0.7877 (ttp-110) cc_final: 0.7647 (mtp-110) REVERT: w 226 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7327 (mt-10) REVERT: w 261 ARG cc_start: 0.7222 (tmm-80) cc_final: 0.6849 (tmm-80) outliers start: 68 outliers final: 22 residues processed: 705 average time/residue: 0.8006 time to fit residues: 669.6675 Evaluate side-chains 685 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 650 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain V residue 44 LYS Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain e residue 54 ARG Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 38 GLU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 150 ARG Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 253 GLU Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain u residue 109 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 51 optimal weight: 3.9990 chunk 376 optimal weight: 0.6980 chunk 273 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 427 optimal weight: 7.9990 chunk 399 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 288 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 chunk 401 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 11 ASN Z 60 ASN e 65 ASN f 61 GLN p 53 ASN p 124 GLN p 141 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.098785 restraints weight = 43186.584| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.02 r_work: 0.2832 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9125 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 40724 Z= 0.164 Angle : 0.607 12.102 54924 Z= 0.308 Chirality : 0.043 0.241 5933 Planarity : 0.005 0.057 6671 Dihedral : 13.671 160.642 6450 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.24 % Favored : 96.68 % Rotamer: Outliers : 1.71 % Allowed : 13.75 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 2.06 (0.12), residues: 4667 helix: 2.20 (0.09), residues: 3013 sheet: -0.86 (0.91), residues: 23 loop : -0.15 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG w 51 TYR 0.023 0.002 TYR w 129 PHE 0.030 0.002 PHE i 292 TRP 0.021 0.002 TRP u 86 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (40713) covalent geometry : angle 0.60619 / 0.31 (54908) SS BOND : bond 0.00410 / 0.27 ( 8) SS BOND : angle 1.81892 / 1.12 ( 16) hydrogen bonds : bond 0.05990 / 4.07 ( 2314) hydrogen bonds : angle 4.20835 / 3.01 ( 6738) Misc. bond : bond 0.00074 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 652 time to evaluate : 1.449 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: V 6 LEU cc_start: 0.8076 (mt) cc_final: 0.7326 (tp) REVERT: V 8 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7607 (ttmm) REVERT: V 120 LEU cc_start: 0.8827 (tp) cc_final: 0.8416 (mt) REVERT: X 105 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8382 (mpp) REVERT: X 151 LYS cc_start: 0.9025 (tppp) cc_final: 0.8680 (tptm) REVERT: Y 90 SER cc_start: 0.8550 (m) cc_final: 0.8263 (p) REVERT: Z 61 VAL cc_start: 0.8627 (m) cc_final: 0.8263 (p) REVERT: a 72 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8327 (ttm170) REVERT: b 35 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8277 (mt) REVERT: c 85 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8646 (mt-10) REVERT: d 168 LYS cc_start: 0.8009 (tmmt) cc_final: 0.7653 (ttmm) REVERT: e 54 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.5359 (mmt90) REVERT: e 116 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: h 37 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8399 (tt0) REVERT: h 53 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: i 69 MET cc_start: 0.9182 (mtp) cc_final: 0.8951 (mtp) REVERT: i 278 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8368 (tpt) REVERT: i 321 LYS cc_start: 0.8069 (tppt) cc_final: 0.7686 (mmmm) REVERT: i 324 LYS cc_start: 0.8201 (tptt) cc_final: 0.7941 (tptt) REVERT: l 387 THR cc_start: 0.9094 (t) cc_final: 0.8740 (m) REVERT: n 53 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8119 (pt0) REVERT: o 111 LYS cc_start: 0.8406 (mttt) cc_final: 0.8200 (mttp) REVERT: p 13 GLN cc_start: 0.8340 (tt0) cc_final: 0.7721 (mp10) REVERT: p 65 ARG cc_start: 0.8455 (mtp180) cc_final: 0.7955 (mtp-110) REVERT: p 66 GLN cc_start: 0.8469 (mt0) cc_final: 0.8148 (mp10) REVERT: p 150 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7619 (mmt180) REVERT: r 454 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.8671 (pp) REVERT: s 200 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8569 (mm) REVERT: s 227 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: s 251 THR cc_start: 0.8263 (m) cc_final: 0.7790 (t) REVERT: s 253 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: u 6 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6936 (tm-30) REVERT: u 11 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7630 (tp30) REVERT: u 84 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: u 109 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6370 (tt0) REVERT: v 15 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8215 (mtpm) REVERT: v 36 GLU cc_start: 0.7319 (pt0) cc_final: 0.6845 (pt0) REVERT: w 226 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7322 (mt-10) REVERT: w 261 ARG cc_start: 0.7244 (tmm-80) cc_final: 0.6869 (tmm-80) outliers start: 70 outliers final: 30 residues processed: 685 average time/residue: 0.8119 time to fit residues: 656.7560 Evaluate side-chains 691 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 643 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain V residue 44 LYS Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 54 ARG Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 53 GLU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 150 ARG Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 253 GLU Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain u residue 109 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 83 optimal weight: 0.7980 chunk 277 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 395 optimal weight: 0.9980 chunk 240 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 329 optimal weight: 5.9990 chunk 434 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 454 optimal weight: 0.6980 chunk 202 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 11 ASN W 85 GLN W 90 ASN f 61 GLN h 27 HIS i 150 ASN p 53 ASN p 141 GLN r 139 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.124104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.102327 restraints weight = 43255.662| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.04 r_work: 0.2878 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 40724 Z= 0.117 Angle : 0.544 11.964 54924 Z= 0.275 Chirality : 0.039 0.202 5933 Planarity : 0.004 0.053 6671 Dihedral : 13.129 155.126 6450 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.81 % Favored : 97.11 % Rotamer: Outliers : 1.27 % Allowed : 14.24 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.12), residues: 4667 helix: 2.33 (0.09), residues: 3013 sheet: -0.62 (0.91), residues: 25 loop : -0.10 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG w 51 TYR 0.022 0.001 TYR l 422 PHE 0.031 0.001 PHE i 292 TRP 0.023 0.001 TRP l 144 HIS 0.005 0.001 HIS r 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (40713) covalent geometry : angle 0.54355 / 0.28 (54908) SS BOND : bond 0.00311 / 0.21 ( 8) SS BOND : angle 1.48398 / 0.91 ( 16) hydrogen bonds : bond 0.04860 / 3.31 ( 2314) hydrogen bonds : angle 4.07947 / 2.92 ( 6738) Misc. bond : bond 0.00041 / 0.02 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 659 time to evaluate : 1.347 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: V 6 LEU cc_start: 0.8074 (mt) cc_final: 0.7338 (tp) REVERT: V 8 LYS cc_start: 0.7809 (mtmt) cc_final: 0.7535 (ttmm) REVERT: V 120 LEU cc_start: 0.8833 (tp) cc_final: 0.8424 (mt) REVERT: X 151 LYS cc_start: 0.8995 (tppp) cc_final: 0.8668 (tptm) REVERT: Y 90 SER cc_start: 0.8581 (m) cc_final: 0.8319 (p) REVERT: Z 61 VAL cc_start: 0.8597 (m) cc_final: 0.8210 (p) REVERT: a 72 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8318 (ttm170) REVERT: c 85 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8639 (mt-10) REVERT: d 168 LYS cc_start: 0.8020 (tmmt) cc_final: 0.7688 (ttmm) REVERT: e 54 ARG cc_start: 0.6182 (OUTLIER) cc_final: 0.5274 (mmt90) REVERT: h 37 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: h 53 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: i 69 MET cc_start: 0.9165 (mtp) cc_final: 0.8941 (mtp) REVERT: i 278 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8170 (tpt) REVERT: i 321 LYS cc_start: 0.8044 (tppt) cc_final: 0.7634 (mmmm) REVERT: i 324 LYS cc_start: 0.8165 (tptt) cc_final: 0.7908 (tptt) REVERT: l 387 THR cc_start: 0.9000 (t) cc_final: 0.8656 (m) REVERT: l 581 LYS cc_start: 0.8640 (mttt) cc_final: 0.8347 (mtmt) REVERT: o 111 LYS cc_start: 0.8388 (mttt) cc_final: 0.8188 (mttp) REVERT: p 13 GLN cc_start: 0.8297 (tt0) cc_final: 0.7713 (mp10) REVERT: p 65 ARG cc_start: 0.8456 (mtp180) cc_final: 0.7984 (mtp-110) REVERT: p 66 GLN cc_start: 0.8483 (mt0) cc_final: 0.8196 (mp10) REVERT: p 150 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7621 (mmt180) REVERT: s 200 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8592 (mm) REVERT: s 227 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: s 251 THR cc_start: 0.8190 (m) cc_final: 0.7740 (t) REVERT: s 253 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7882 (pm20) REVERT: u 6 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: u 11 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7669 (tp30) REVERT: u 84 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: u 109 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6358 (tt0) REVERT: v 15 LYS cc_start: 0.8303 (mtpp) cc_final: 0.8102 (mtpm) REVERT: v 36 GLU cc_start: 0.7369 (pt0) cc_final: 0.6869 (pt0) REVERT: v 115 ARG cc_start: 0.7726 (mtp-110) cc_final: 0.7461 (mtp-110) REVERT: w 226 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7316 (mt-10) REVERT: w 261 ARG cc_start: 0.7210 (tmm-80) cc_final: 0.6837 (tmm-80) outliers start: 52 outliers final: 26 residues processed: 687 average time/residue: 0.8130 time to fit residues: 661.4488 Evaluate side-chains 688 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 649 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain V residue 44 LYS Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 54 ARG Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 38 GLU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 150 ARG Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 253 GLU Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain u residue 109 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 323 optimal weight: 7.9990 chunk 302 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 172 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 371 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 440 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 85 GLN W 90 ASN Z 60 ASN e 65 ASN f 61 GLN m 46 ASN p 53 ASN p 124 GLN p 141 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.120798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.098997 restraints weight = 43190.925| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.01 r_work: 0.2816 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 40724 Z= 0.181 Angle : 0.657 24.395 54924 Z= 0.338 Chirality : 0.044 0.247 5933 Planarity : 0.005 0.108 6671 Dihedral : 13.353 156.271 6450 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 1.39 % Allowed : 14.14 % Favored : 84.47 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.12), residues: 4667 helix: 2.15 (0.09), residues: 3013 sheet: -0.74 (0.91), residues: 23 loop : -0.15 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG w 51 TYR 0.024 0.002 TYR w 129 PHE 0.230 0.002 PHE l 498 TRP 0.021 0.002 TRP u 86 HIS 0.008 0.001 HIS r 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (40713) covalent geometry : angle 0.65592 / 0.34 (54908) SS BOND : bond 0.00429 / 0.29 ( 8) SS BOND : angle 1.84965 / 1.14 ( 16) hydrogen bonds : bond 0.06222 / 4.22 ( 2314) hydrogen bonds : angle 4.24876 / 3.04 ( 6738) Misc. bond : bond 0.00066 / 0.03 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18875.86 seconds wall clock time: 320 minutes 41.09 seconds (19241.09 seconds total)