Starting phenix.real_space_refine on Sat Mar 7 09:01:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vbl_31881/03_2026/7vbl_31881.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbl_31881/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vbl_31881/03_2026/7vbl_31881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbl_31881/03_2026/7vbl_31881.map" model { file = "/net/cci-nas-00/data/ceres_data/7vbl_31881/03_2026/7vbl_31881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbl_31881/03_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.75, per 1000 atoms: 0.22 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: 3.63 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: 1.28 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: 7.22 Time building geometry restraints manager: 4.78 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: 23928 35.72 - 71.44: 889 71.44 - 107.16: 65 107.16 - 142.87: 32 142.87 - 178.59: 12 Dihedral angle restraints: 24926 sinusoidal: 11067 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 24923 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.290 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 35.370 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 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 : 18.446 178.593 15946 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 covalent geometry : bond 0.00966 (40713) covalent geometry : angle 1.09169 (54908) SS BOND : bond 0.06218 ( 8) SS BOND : angle 2.97545 ( 16) hydrogen bonds : bond 0.14899 ( 2314) hydrogen bonds : angle 5.54651 ( 6738) Misc. bond : bond 0.60124 ( 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 : 1.467 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: 0.7870 (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: 0.9241 time to fit residues: 985.2217 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 : 1.567 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3351 r_free = 0.3351 target = 0.126115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.102138 restraints weight = 43517.778| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.02 r_work: 0.2921 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40724 Z= 0.139 Angle : 0.611 13.709 54924 Z= 0.311 Chirality : 0.041 0.187 5933 Planarity : 0.005 0.051 6671 Dihedral : 18.682 179.823 6759 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.81 % Rotamer: Outliers : 2.10 % Allowed : 9.17 % 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: 1.19 (0.12), residues: 4667 helix: 1.61 (0.09), residues: 3001 sheet: -1.62 (0.88), residues: 25 loop : -0.67 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG w 51 TYR 0.026 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 covalent geometry : bond 0.00286 (40713) covalent geometry : angle 0.61025 (54908) SS BOND : bond 0.00484 ( 8) SS BOND : angle 2.02182 ( 16) hydrogen bonds : bond 0.05696 ( 2314) hydrogen bonds : angle 4.41942 ( 6738) Misc. bond : bond 0.00722 ( 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 798 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 712 time to evaluate : 1.596 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: Q 56 LYS cc_start: 0.7923 (pttt) cc_final: 0.7300 (mmmt) REVERT: U 71 GLN cc_start: 0.8364 (mt0) cc_final: 0.8135 (mt0) REVERT: V 8 LYS cc_start: 0.7870 (mtmt) cc_final: 0.6737 (tmtt) REVERT: V 120 LEU cc_start: 0.8711 (tp) cc_final: 0.8260 (mt) REVERT: W 93 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7466 (tp30) REVERT: X 151 LYS cc_start: 0.8876 (tppp) cc_final: 0.8569 (tptm) REVERT: Y 90 SER cc_start: 0.8315 (m) cc_final: 0.7971 (p) REVERT: a 72 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8412 (ttm170) REVERT: a 148 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7982 (pp20) REVERT: c 36 MET cc_start: 0.8113 (mmp) cc_final: 0.7373 (mtt) REVERT: d 78 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: e 54 ARG cc_start: 0.6235 (OUTLIER) cc_final: 0.5273 (mmt90) REVERT: h 53 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: h 55 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8493 (mt-10) REVERT: i 69 MET cc_start: 0.9157 (mtp) cc_final: 0.8919 (mtp) REVERT: i 278 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8271 (tpt) REVERT: i 321 LYS cc_start: 0.7657 (tppt) cc_final: 0.7360 (mmmm) REVERT: j 16 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8284 (mp) REVERT: j 19 LEU cc_start: 0.8615 (tp) cc_final: 0.8249 (mm) REVERT: k 1 MET cc_start: 0.6854 (mtp) cc_final: 0.6376 (ttp) REVERT: k 10 MET cc_start: 0.9088 (tpt) cc_final: 0.8819 (tpt) REVERT: l 55 MET cc_start: 0.9106 (mtp) cc_final: 0.8887 (mtt) REVERT: l 267 MET cc_start: 0.8548 (mmm) cc_final: 0.8270 (mmm) REVERT: l 496 MET cc_start: 0.8235 (mtp) cc_final: 0.7640 (tmm) REVERT: o 111 LYS cc_start: 0.8356 (mttt) cc_final: 0.8103 (mttp) REVERT: p 13 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7484 (mp10) REVERT: p 59 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7594 (tttp) REVERT: p 124 GLN cc_start: 0.8376 (mt0) cc_final: 0.8176 (mt0) REVERT: r 22 MET cc_start: 0.9038 (mmm) cc_final: 0.8826 (mmp) REVERT: r 398 MET cc_start: 0.8697 (mtp) cc_final: 0.8475 (mtm) REVERT: s 258 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8331 (t0) REVERT: u 19 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7459 (ptpt) REVERT: u 76 ARG cc_start: 0.7334 (ttm110) cc_final: 0.7081 (ttp80) REVERT: u 80 GLU cc_start: 0.6653 (tp30) cc_final: 0.5752 (tp30) REVERT: u 84 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: w 51 ARG cc_start: 0.7678 (ptp-110) cc_final: 0.6784 (ttp-110) REVERT: w 72 ARG cc_start: 0.7769 (ttp-170) cc_final: 0.7537 (ttt180) REVERT: w 264 GLU cc_start: 0.7618 (mp0) cc_final: 0.7392 (mp0) outliers start: 86 outliers final: 22 residues processed: 743 average time/residue: 0.9242 time to fit residues: 807.0719 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 : 1.480 ------------------------------------------------------------------------------- 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 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 148 GLU 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 h residue 55 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 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 m residue 137 SER 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 169 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 250 optimal weight: 3.9990 chunk 416 optimal weight: 0.4980 chunk 408 optimal weight: 0.0370 chunk 272 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 107 GLN w 239 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.126261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.104344 restraints weight = 43393.184| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.06 r_work: 0.2909 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40724 Z= 0.124 Angle : 0.553 9.819 54924 Z= 0.282 Chirality : 0.040 0.189 5933 Planarity : 0.004 0.044 6671 Dihedral : 17.274 177.791 6747 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 2.34 % Allowed : 10.92 % Favored : 86.74 % 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: 1.79 (0.12), residues: 4667 helix: 2.07 (0.09), residues: 2996 sheet: -1.12 (0.86), residues: 25 loop : -0.41 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG p 65 TYR 0.023 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 covalent geometry : bond 0.00257 (40713) covalent geometry : angle 0.55283 (54908) SS BOND : bond 0.00342 ( 8) SS BOND : angle 1.52256 ( 16) hydrogen bonds : bond 0.05158 ( 2314) hydrogen bonds : angle 4.19059 ( 6738) Misc. bond : bond 0.00099 ( 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: 96 poor density : 701 time to evaluate : 1.709 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: U 71 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8152 (mt0) REVERT: V 120 LEU cc_start: 0.8775 (tp) cc_final: 0.8330 (mt) REVERT: W 52 LYS cc_start: 0.8277 (mtmt) cc_final: 0.8055 (ttpt) REVERT: W 93 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7554 (tp30) REVERT: W 120 MET cc_start: 0.7342 (ttp) cc_final: 0.7052 (ttp) REVERT: Y 90 SER cc_start: 0.8404 (m) cc_final: 0.8050 (p) REVERT: Z 49 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7537 (mm-30) REVERT: a 72 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8280 (ttm170) REVERT: a 106 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8508 (t) REVERT: c 36 MET cc_start: 0.8042 (mmp) cc_final: 0.7326 (mtt) REVERT: e 54 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.5368 (mmt90) REVERT: h 53 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: i 40 MET cc_start: 0.9221 (tpt) cc_final: 0.8940 (mmm) REVERT: i 69 MET cc_start: 0.9163 (mtp) cc_final: 0.8958 (mtp) REVERT: i 278 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8295 (tpt) REVERT: i 321 LYS cc_start: 0.7771 (tppt) cc_final: 0.7417 (mmmm) REVERT: j 16 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8202 (mm) REVERT: j 19 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8278 (mm) REVERT: k 1 MET cc_start: 0.7210 (mtp) cc_final: 0.6908 (ttp) REVERT: o 111 LYS cc_start: 0.8354 (mttt) cc_final: 0.8117 (mttp) REVERT: p 13 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7584 (mp10) REVERT: p 66 GLN cc_start: 0.8397 (mt0) cc_final: 0.8097 (mp10) REVERT: p 124 GLN cc_start: 0.8461 (mt0) cc_final: 0.8244 (mt0) REVERT: r 114 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: r 398 MET cc_start: 0.8696 (mtp) cc_final: 0.8468 (mtm) REVERT: s 103 LEU cc_start: 0.8502 (tp) cc_final: 0.8280 (mt) REVERT: s 143 GLU cc_start: 0.8646 (tp30) cc_final: 0.8370 (tm-30) REVERT: s 253 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7453 (pm20) REVERT: u 6 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6933 (tm-30) REVERT: u 76 ARG cc_start: 0.7343 (ttm110) cc_final: 0.7125 (ttp80) REVERT: u 109 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6290 (tm-30) REVERT: v 115 ARG cc_start: 0.7493 (ttp-110) cc_final: 0.7181 (mtp-110) REVERT: w 72 ARG cc_start: 0.7893 (ttp-170) cc_final: 0.7495 (ttp80) REVERT: w 251 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7330 (mt-10) outliers start: 96 outliers final: 26 residues processed: 742 average time/residue: 0.8868 time to fit residues: 773.7068 Evaluate side-chains 695 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 654 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain S residue 54 ILE 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 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 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: 0.9990 chunk 89 optimal weight: 0.7980 chunk 344 optimal weight: 0.4980 chunk 417 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 336 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 296 optimal weight: 4.9990 chunk 440 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 p 141 GLN r 139 GLN r 304 GLN u 104 GLN w 132 GLN w 239 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.127566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.106154 restraints weight = 43444.379| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 0.99 r_work: 0.2940 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 40724 Z= 0.111 Angle : 0.534 12.081 54924 Z= 0.269 Chirality : 0.039 0.183 5933 Planarity : 0.004 0.042 6671 Dihedral : 16.393 178.502 6747 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.96 % Rotamer: Outliers : 2.27 % Allowed : 11.53 % Favored : 86.20 % 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: 2.09 (0.12), residues: 4667 helix: 2.28 (0.09), residues: 2998 sheet: -0.76 (0.89), residues: 25 loop : -0.24 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG w 51 TYR 0.027 0.001 TYR d 32 PHE 0.030 0.001 PHE i 292 TRP 0.020 0.001 TRP u 86 HIS 0.006 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00227 (40713) covalent geometry : angle 0.53374 (54908) SS BOND : bond 0.00267 ( 8) SS BOND : angle 1.22025 ( 16) hydrogen bonds : bond 0.04618 ( 2314) hydrogen bonds : angle 4.05189 ( 6738) Misc. bond : bond 0.00033 ( 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 800 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 707 time to evaluate : 1.564 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7353 (mmm) REVERT: S 48 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8554 (mtm) REVERT: U 71 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8215 (mt0) REVERT: V 120 LEU cc_start: 0.8793 (tp) cc_final: 0.8344 (mt) REVERT: W 52 LYS cc_start: 0.8248 (mtmt) cc_final: 0.7890 (ttpp) REVERT: W 93 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7481 (tp30) REVERT: X 151 LYS cc_start: 0.8871 (tppp) cc_final: 0.8578 (tptm) REVERT: Y 90 SER cc_start: 0.8433 (m) cc_final: 0.8084 (p) REVERT: Z 49 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: Z 61 VAL cc_start: 0.8613 (m) cc_final: 0.8283 (p) REVERT: a 72 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8262 (ttm170) REVERT: b 35 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8242 (mt) REVERT: c 36 MET cc_start: 0.7943 (mmp) cc_final: 0.7324 (mtt) REVERT: c 85 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8538 (mt-10) REVERT: e 54 ARG cc_start: 0.6264 (OUTLIER) cc_final: 0.5328 (mmt90) REVERT: h 53 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8523 (tt0) REVERT: i 278 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8113 (tpt) REVERT: i 321 LYS cc_start: 0.7744 (tppt) cc_final: 0.7461 (mmmm) REVERT: j 16 LEU cc_start: 0.8665 (tp) cc_final: 0.8205 (mm) REVERT: j 19 LEU cc_start: 0.8673 (tp) cc_final: 0.8296 (mm) REVERT: k 1 MET cc_start: 0.7349 (mtp) cc_final: 0.7068 (ttp) REVERT: k 10 MET cc_start: 0.9082 (tpt) cc_final: 0.8827 (tpt) REVERT: m 5 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7975 (mt) REVERT: p 13 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7608 (mp10) REVERT: p 65 ARG cc_start: 0.8412 (mtp180) cc_final: 0.7919 (mtp-110) REVERT: p 66 GLN cc_start: 0.8414 (mt0) cc_final: 0.8104 (mp10) REVERT: p 150 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7544 (mmt180) REVERT: r 47 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6975 (mm-30) REVERT: r 398 MET cc_start: 0.8660 (mtp) cc_final: 0.8436 (mtm) REVERT: s 103 LEU cc_start: 0.8469 (tp) cc_final: 0.8266 (mt) REVERT: u 6 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: u 19 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7415 (ptpt) REVERT: u 84 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: u 109 GLU cc_start: 0.6513 (tt0) cc_final: 0.6267 (tm-30) REVERT: v 115 ARG cc_start: 0.7625 (ttp-110) cc_final: 0.7204 (mtp-110) REVERT: w 251 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7316 (mt-10) outliers start: 93 outliers final: 33 residues processed: 748 average time/residue: 0.8894 time to fit residues: 783.5937 Evaluate side-chains 708 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 658 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 52 MET 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 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 Z residue 49 GLU Chi-restraints excluded: chain a residue 72 ARG 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 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 h residue 53 GLU Chi-restraints excluded: chain h residue 73 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 38 GLU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain o residue 83 THR 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 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 151 LEU Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 19 LYS Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain w residue 251 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: 4.9990 chunk 422 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 415 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 443 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 319 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 31 ASN U 11 ASN U 71 GLN W 85 GLN W 90 ASN Z 48 ASN c 160 GLN e 65 ASN e 145 ASN f 61 GLN l 34 ASN l 136 ASN l 170 GLN l 579 ASN o 79 ASN p 141 GLN p 169 HIS r 139 GLN r 304 GLN v 65 GLN w 202 HIS w 239 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.119436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.097030 restraints weight = 42935.920| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.06 r_work: 0.2789 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 40724 Z= 0.226 Angle : 0.687 14.390 54924 Z= 0.349 Chirality : 0.047 0.214 5933 Planarity : 0.005 0.054 6671 Dihedral : 16.742 179.938 6744 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.47 % Favored : 96.42 % Rotamer: Outliers : 2.90 % Allowed : 11.90 % Favored : 85.20 % 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: 1.77 (0.12), residues: 4667 helix: 1.98 (0.09), residues: 2998 sheet: -0.83 (0.92), residues: 25 loop : -0.27 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG d 43 TYR 0.028 0.002 TYR w 129 PHE 0.026 0.002 PHE i 292 TRP 0.021 0.002 TRP u 86 HIS 0.012 0.002 HIS l 534 Details of bonding type rmsd covalent geometry : bond 0.00540 (40713) covalent geometry : angle 0.68584 (54908) SS BOND : bond 0.01115 ( 8) SS BOND : angle 2.46047 ( 16) hydrogen bonds : bond 0.07112 ( 2314) hydrogen bonds : angle 4.37993 ( 6738) Misc. bond : bond 0.00143 ( 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 792 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 673 time to evaluate : 1.938 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: V 8 LYS cc_start: 0.7953 (mtmt) cc_final: 0.6996 (tmtt) REVERT: V 120 LEU cc_start: 0.8837 (tp) cc_final: 0.8408 (mt) REVERT: W 52 LYS cc_start: 0.8408 (mtmt) cc_final: 0.8032 (ttpp) REVERT: W 93 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7738 (tp30) REVERT: Y 90 SER cc_start: 0.8508 (m) cc_final: 0.8165 (p) REVERT: Z 61 VAL cc_start: 0.8738 (m) cc_final: 0.8337 (p) REVERT: a 72 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8391 (ttm170) REVERT: b 35 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8340 (mt) REVERT: c 36 MET cc_start: 0.8122 (mmp) cc_final: 0.7462 (mtt) REVERT: c 85 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8672 (mt-10) REVERT: e 54 ARG cc_start: 0.6275 (OUTLIER) cc_final: 0.5372 (mmt90) REVERT: e 116 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: e 145 ASN cc_start: 0.8632 (m110) cc_final: 0.8333 (m110) REVERT: h 53 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8615 (tt0) REVERT: i 274 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8545 (mp0) REVERT: i 278 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8491 (tpt) REVERT: i 321 LYS cc_start: 0.7961 (tppt) cc_final: 0.7607 (mmmm) REVERT: j 1 MET cc_start: 0.7473 (tmt) cc_final: 0.6922 (tpt) REVERT: k 10 MET cc_start: 0.9160 (tpt) cc_final: 0.8886 (tpt) REVERT: l 59 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: n 41 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8820 (mttt) REVERT: n 53 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8224 (pt0) REVERT: p 13 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8184 (tm-30) REVERT: p 59 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8327 (tttp) REVERT: p 65 ARG cc_start: 0.8488 (mtp180) cc_final: 0.7984 (mtp-110) REVERT: p 66 GLN cc_start: 0.8482 (mt0) cc_final: 0.8158 (mp10) REVERT: p 150 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7663 (mmt180) REVERT: r 454 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.8680 (pp) REVERT: s 143 GLU cc_start: 0.8678 (tp30) cc_final: 0.8446 (tm-30) REVERT: s 227 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: s 251 THR cc_start: 0.8313 (m) cc_final: 0.7893 (t) REVERT: u 6 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6991 (tm-30) REVERT: u 84 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: u 109 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6261 (tt0) REVERT: v 54 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8407 (pt0) REVERT: v 115 ARG cc_start: 0.7772 (ttp-110) cc_final: 0.7545 (mtp-110) REVERT: w 330 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8671 (ttmt) REVERT: w 354 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8753 (mp) outliers start: 119 outliers final: 47 residues processed: 725 average time/residue: 0.9755 time to fit residues: 831.2146 Evaluate side-chains 720 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 651 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 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 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 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 55 LEU Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 138 GLU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 73 MET Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain i residue 274 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 59 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 316 THR Chi-restraints excluded: chain l residue 387 THR 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 8 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 53 GLU Chi-restraints excluded: chain n residue 58 LYS 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 r residue 58 SER 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 201 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 84 GLU Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain v residue 34 ARG Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 94 ASP 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: 7.9990 chunk 202 optimal weight: 6.9990 chunk 369 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 379 optimal weight: 4.9990 chunk 307 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 265 optimal weight: 6.9990 chunk 326 optimal weight: 3.9990 chunk 452 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 w 239 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.098645 restraints weight = 43265.129| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.04 r_work: 0.2827 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 40724 Z= 0.158 Angle : 0.600 12.045 54924 Z= 0.306 Chirality : 0.042 0.201 5933 Planarity : 0.005 0.049 6671 Dihedral : 16.259 174.807 6744 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.09 % Favored : 96.81 % Rotamer: Outliers : 2.58 % Allowed : 12.51 % Favored : 84.91 % 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: 1.90 (0.12), residues: 4667 helix: 2.09 (0.09), residues: 3006 sheet: -0.79 (0.90), residues: 25 loop : -0.24 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG w 51 TYR 0.022 0.002 TYR w 129 PHE 0.030 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 covalent geometry : bond 0.00359 (40713) covalent geometry : angle 0.59877 (54908) SS BOND : bond 0.00420 ( 8) SS BOND : angle 2.33094 ( 16) hydrogen bonds : bond 0.06003 ( 2314) hydrogen bonds : angle 4.24981 ( 6738) Misc. bond : bond 0.00058 ( 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 768 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 662 time to evaluate : 1.542 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: 0.8826 (OUTLIER) cc_final: 0.8411 (mp0) REVERT: V 8 LYS cc_start: 0.7907 (mtmt) cc_final: 0.7005 (tmtt) REVERT: V 120 LEU cc_start: 0.8849 (tp) cc_final: 0.8395 (mt) REVERT: W 52 LYS cc_start: 0.8372 (mtmt) cc_final: 0.8017 (ttpp) REVERT: W 93 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: X 105 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.7939 (mpp) REVERT: X 151 LYS cc_start: 0.8998 (tppp) cc_final: 0.8649 (tptm) REVERT: Y 90 SER cc_start: 0.8530 (m) cc_final: 0.8200 (p) REVERT: Z 61 VAL cc_start: 0.8648 (m) cc_final: 0.8317 (p) REVERT: a 72 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8318 (ttm170) REVERT: c 36 MET cc_start: 0.8056 (mmp) cc_final: 0.7449 (mtt) REVERT: c 85 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8647 (mt-10) REVERT: d 168 LYS cc_start: 0.7981 (tmmt) cc_final: 0.7616 (ttmm) REVERT: e 54 ARG cc_start: 0.6137 (OUTLIER) cc_final: 0.5272 (mmt90) REVERT: e 116 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: h 53 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8583 (tt0) REVERT: i 278 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8389 (tpt) REVERT: i 321 LYS cc_start: 0.7963 (tppt) cc_final: 0.7609 (mmmm) REVERT: j 1 MET cc_start: 0.7422 (tmt) cc_final: 0.6988 (tpt) REVERT: j 19 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8271 (mm) REVERT: k 10 MET cc_start: 0.9094 (tpt) cc_final: 0.8809 (tpt) REVERT: n 41 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8810 (mttt) REVERT: p 59 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8238 (tttp) REVERT: p 65 ARG cc_start: 0.8470 (mtp180) cc_final: 0.7956 (mtp-110) REVERT: p 66 GLN cc_start: 0.8453 (mt0) cc_final: 0.8132 (mp10) REVERT: p 150 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7522 (mmt180) REVERT: r 45 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7679 (mt) REVERT: r 454 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.8745 (pp) REVERT: s 143 GLU cc_start: 0.8631 (tp30) cc_final: 0.8409 (tm-30) REVERT: s 202 GLU cc_start: 0.7987 (tp30) cc_final: 0.7776 (tt0) REVERT: s 227 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: s 251 THR cc_start: 0.8219 (m) cc_final: 0.7841 (t) REVERT: s 258 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8428 (t0) REVERT: u 6 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: u 80 GLU cc_start: 0.6892 (tp30) cc_final: 0.5937 (tp30) REVERT: u 84 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: u 109 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6256 (tt0) REVERT: v 54 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8332 (pt0) REVERT: w 171 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8275 (tp30) REVERT: w 251 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: w 264 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6870 (mm-30) REVERT: w 330 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8677 (ttmt) REVERT: w 354 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8753 (mp) outliers start: 106 outliers final: 40 residues processed: 708 average time/residue: 0.9679 time to fit residues: 803.4938 Evaluate side-chains 715 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 649 time to evaluate : 1.576 ------------------------------------------------------------------------------- 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 93 GLU Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain a residue 72 ARG 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 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 h residue 53 GLU Chi-restraints excluded: chain h residue 74 LYS 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 493 VAL Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 3 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 8 VAL 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 59 LYS Chi-restraints excluded: chain p residue 150 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 58 SER 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 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 54 GLN Chi-restraints excluded: chain w residue 171 GLU Chi-restraints excluded: chain w residue 251 GLU Chi-restraints excluded: chain w residue 254 GLU Chi-restraints excluded: chain w residue 264 GLU Chi-restraints excluded: chain w residue 330 LYS Chi-restraints excluded: chain w residue 354 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 16 optimal weight: 4.9990 chunk 438 optimal weight: 7.9990 chunk 103 optimal weight: 0.0020 chunk 9 optimal weight: 7.9990 chunk 362 optimal weight: 10.0000 chunk 402 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 chunk 443 optimal weight: 0.3980 chunk 135 optimal weight: 8.9990 overall best weight: 2.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 11 ASN W 85 GLN W 90 ASN e 145 ASN f 61 GLN p 13 GLN p 53 ASN p 124 GLN p 141 GLN r 139 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 = 0.3269 r_free = 0.3269 target = 0.119989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.097644 restraints weight = 43184.547| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 0.99 r_work: 0.2809 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 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 = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 40724 Z= 0.177 Angle : 0.627 13.133 54924 Z= 0.319 Chirality : 0.044 0.220 5933 Planarity : 0.005 0.049 6671 Dihedral : 16.080 170.883 6744 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.45 % Favored : 96.44 % Rotamer: Outliers : 2.44 % Allowed : 12.82 % Favored : 84.74 % 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: 1.86 (0.12), residues: 4667 helix: 2.05 (0.09), residues: 3006 sheet: -0.81 (0.92), residues: 25 loop : -0.25 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG w 51 TYR 0.024 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 covalent geometry : bond 0.00412 (40713) covalent geometry : angle 0.62636 (54908) SS BOND : bond 0.00443 ( 8) SS BOND : angle 1.96945 ( 16) hydrogen bonds : bond 0.06396 ( 2314) hydrogen bonds : angle 4.29394 ( 6738) Misc. bond : bond 0.00081 ( 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 760 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 660 time to evaluate : 1.676 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: 0.8841 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: V 6 LEU cc_start: 0.8081 (mt) cc_final: 0.7320 (tp) REVERT: V 8 LYS cc_start: 0.7911 (mtmt) cc_final: 0.7019 (tmtt) REVERT: V 120 LEU cc_start: 0.8855 (tp) cc_final: 0.8408 (mt) REVERT: W 52 LYS cc_start: 0.8392 (mtmt) cc_final: 0.8034 (ttpp) REVERT: X 151 LYS cc_start: 0.9002 (tppp) cc_final: 0.8655 (tptm) REVERT: Y 90 SER cc_start: 0.8556 (m) cc_final: 0.8236 (p) REVERT: Z 61 VAL cc_start: 0.8659 (m) cc_final: 0.8305 (p) REVERT: a 72 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8344 (ttm170) REVERT: c 85 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8665 (mt-10) REVERT: d 6 ASP cc_start: 0.8656 (t0) cc_final: 0.8448 (t0) REVERT: d 168 LYS cc_start: 0.8001 (tmmt) cc_final: 0.7637 (ttmm) REVERT: e 54 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5329 (mmt90) REVERT: e 116 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: e 145 ASN cc_start: 0.8648 (m110) cc_final: 0.8315 (m110) REVERT: h 37 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: h 53 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8592 (tt0) REVERT: i 278 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8435 (tpt) REVERT: i 321 LYS cc_start: 0.8049 (tppt) cc_final: 0.7661 (mmmm) REVERT: j 1 MET cc_start: 0.7444 (tmt) cc_final: 0.6999 (tpt) REVERT: k 10 MET cc_start: 0.9109 (tpt) cc_final: 0.8834 (tpt) REVERT: n 41 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8829 (mttt) REVERT: p 59 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8261 (tttp) REVERT: p 65 ARG cc_start: 0.8491 (mtp180) cc_final: 0.7983 (mtp-110) REVERT: p 66 GLN cc_start: 0.8487 (mt0) cc_final: 0.8165 (mp10) REVERT: p 150 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7524 (mmt180) REVERT: r 45 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7731 (mt) REVERT: r 454 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.8691 (pp) REVERT: s 143 GLU cc_start: 0.8636 (tp30) cc_final: 0.8419 (tm-30) REVERT: s 227 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: s 251 THR cc_start: 0.8245 (m) cc_final: 0.7798 (t) REVERT: s 253 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7851 (pm20) REVERT: s 258 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8491 (t0) REVERT: u 6 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6940 (tm-30) REVERT: u 84 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: u 109 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6314 (tt0) REVERT: v 54 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8335 (pt0) REVERT: w 171 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8303 (tp30) outliers start: 100 outliers final: 41 residues processed: 704 average time/residue: 0.9406 time to fit residues: 777.1122 Evaluate side-chains 708 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 646 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 130 GLU Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 186 THR 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 h residue 37 GLU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 74 LYS 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 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 41 LYS 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 59 LYS 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 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 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 v residue 54 GLN Chi-restraints excluded: chain v residue 94 ASP Chi-restraints excluded: chain w residue 171 GLU Chi-restraints excluded: chain w residue 254 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 91 optimal weight: 0.0980 chunk 300 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 438 optimal weight: 0.9980 chunk 332 optimal weight: 0.9980 chunk 294 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 329 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 11 ASN W 85 GLN f 61 GLN p 53 ASN p 141 GLN r 139 GLN r 304 GLN w 239 ASN w 322 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.127004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.105436 restraints weight = 43339.248| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 0.99 r_work: 0.2924 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 40724 Z= 0.110 Angle : 0.527 10.592 54924 Z= 0.266 Chirality : 0.039 0.177 5933 Planarity : 0.004 0.049 6671 Dihedral : 15.231 161.941 6744 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.72 % Favored : 97.21 % Rotamer: Outliers : 1.61 % Allowed : 13.60 % Favored : 84.79 % 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: 2.19 (0.12), residues: 4667 helix: 2.32 (0.09), residues: 3015 sheet: -0.65 (0.90), residues: 25 loop : -0.15 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG w 51 TYR 0.024 0.001 TYR l 422 PHE 0.032 0.001 PHE i 292 TRP 0.025 0.001 TRP l 144 HIS 0.017 0.001 HIS p 12 Details of bonding type rmsd covalent geometry : bond 0.00220 (40713) covalent geometry : angle 0.52707 (54908) SS BOND : bond 0.00312 ( 8) SS BOND : angle 1.32554 ( 16) hydrogen bonds : bond 0.04492 ( 2314) hydrogen bonds : angle 4.05079 ( 6738) Misc. bond : bond 0.00037 ( 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 762 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 696 time to evaluate : 1.339 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: V 120 LEU cc_start: 0.8820 (tp) cc_final: 0.8389 (mt) REVERT: W 93 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7654 (tp30) REVERT: X 151 LYS cc_start: 0.8921 (tppp) cc_final: 0.8610 (tptm) REVERT: Y 90 SER cc_start: 0.8597 (m) cc_final: 0.8303 (p) REVERT: Z 61 VAL cc_start: 0.8600 (m) cc_final: 0.8263 (p) REVERT: a 72 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8273 (ttm170) REVERT: d 6 ASP cc_start: 0.8581 (t0) cc_final: 0.8361 (t0) REVERT: d 168 LYS cc_start: 0.7994 (tmmt) cc_final: 0.7657 (ttmm) REVERT: e 54 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.5208 (mmt90) REVERT: e 116 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: g 51 ARG cc_start: 0.8368 (mmt90) cc_final: 0.8127 (mpt180) REVERT: h 37 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: h 53 GLU cc_start: 0.8775 (tt0) cc_final: 0.8505 (tt0) REVERT: i 278 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8081 (tpt) REVERT: i 321 LYS cc_start: 0.8021 (tppt) cc_final: 0.7624 (mmmm) REVERT: j 1 MET cc_start: 0.7285 (tmt) cc_final: 0.6878 (tpt) REVERT: l 387 THR cc_start: 0.8944 (t) cc_final: 0.8601 (m) REVERT: p 65 ARG cc_start: 0.8410 (mtp180) cc_final: 0.7951 (mtp-110) REVERT: p 66 GLN cc_start: 0.8473 (mt0) cc_final: 0.8187 (mp10) REVERT: p 150 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7572 (mmt180) REVERT: p 176 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6904 (pp20) REVERT: r 45 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7471 (mt) REVERT: s 143 GLU cc_start: 0.8556 (tp30) cc_final: 0.8353 (tm-30) REVERT: s 227 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: s 251 THR cc_start: 0.8170 (m) cc_final: 0.7763 (t) REVERT: s 253 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7796 (pm20) REVERT: u 6 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: u 84 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: u 109 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6267 (tt0) REVERT: v 36 GLU cc_start: 0.7348 (pt0) cc_final: 0.6855 (pt0) outliers start: 66 outliers final: 27 residues processed: 727 average time/residue: 0.8950 time to fit residues: 768.9022 Evaluate side-chains 708 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 667 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 14 MET Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 186 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 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 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 150 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE 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 202 GLU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 253 GLU Chi-restraints excluded: chain s residue 289 LEU 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: 7.9990 chunk 376 optimal weight: 0.8980 chunk 273 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 427 optimal weight: 0.8980 chunk 399 optimal weight: 9.9990 chunk 268 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 401 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 90 ASN Z 60 ASN e 65 ASN e 145 ASN f 61 GLN i 150 ASN m 46 ASN n 3 ASN p 53 ASN p 141 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 = 0.3323 r_free = 0.3323 target = 0.124040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.102113 restraints weight = 43146.317| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.05 r_work: 0.2868 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40724 Z= 0.131 Angle : 0.563 10.790 54924 Z= 0.284 Chirality : 0.041 0.195 5933 Planarity : 0.004 0.060 6671 Dihedral : 15.097 158.311 6743 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.91 % Favored : 97.00 % Rotamer: Outliers : 1.63 % Allowed : 13.82 % Favored : 84.54 % 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: 2.25 (0.12), residues: 4667 helix: 2.35 (0.09), residues: 3013 sheet: -0.51 (0.92), residues: 25 loop : -0.11 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG w 51 TYR 0.019 0.001 TYR l 422 PHE 0.031 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 covalent geometry : bond 0.00286 (40713) covalent geometry : angle 0.56221 (54908) SS BOND : bond 0.00351 ( 8) SS BOND : angle 1.48105 ( 16) hydrogen bonds : bond 0.05192 ( 2314) hydrogen bonds : angle 4.08583 ( 6738) Misc. bond : bond 0.00051 ( 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 731 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 664 time to evaluate : 1.511 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: V 120 LEU cc_start: 0.8828 (tp) cc_final: 0.8397 (mt) REVERT: X 105 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8344 (mpp) REVERT: X 151 LYS cc_start: 0.8933 (tppp) cc_final: 0.8627 (tptm) REVERT: Y 90 SER cc_start: 0.8567 (m) cc_final: 0.8269 (p) REVERT: Z 61 VAL cc_start: 0.8613 (m) cc_final: 0.8255 (p) REVERT: a 72 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8297 (ttm170) REVERT: b 35 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8218 (mt) REVERT: d 6 ASP cc_start: 0.8610 (t0) cc_final: 0.8402 (t0) REVERT: d 168 LYS cc_start: 0.7977 (tmmt) cc_final: 0.7621 (ttmm) REVERT: e 54 ARG cc_start: 0.6224 (OUTLIER) cc_final: 0.5292 (mmt90) REVERT: e 116 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: g 51 ARG cc_start: 0.8494 (mmt90) cc_final: 0.8199 (mpt180) REVERT: h 37 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8370 (tt0) REVERT: h 53 GLU cc_start: 0.8808 (tt0) cc_final: 0.8535 (tt0) REVERT: i 278 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8265 (tpt) REVERT: i 321 LYS cc_start: 0.8014 (tppt) cc_final: 0.7631 (mmmm) REVERT: j 1 MET cc_start: 0.7351 (tmt) cc_final: 0.6921 (tpt) REVERT: k 10 MET cc_start: 0.9132 (tpt) cc_final: 0.8861 (tpt) REVERT: l 387 THR cc_start: 0.9004 (t) cc_final: 0.8630 (m) REVERT: p 13 GLN cc_start: 0.8352 (tt0) cc_final: 0.7703 (mp10) REVERT: p 65 ARG cc_start: 0.8454 (mtp180) cc_final: 0.7977 (mtp-110) REVERT: p 66 GLN cc_start: 0.8469 (mt0) cc_final: 0.8168 (mp10) REVERT: p 150 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7551 (mmt180) REVERT: r 45 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7540 (mt) REVERT: s 143 GLU cc_start: 0.8608 (tp30) cc_final: 0.8389 (tm-30) REVERT: s 200 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8658 (mm) REVERT: s 227 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: s 251 THR cc_start: 0.8203 (m) cc_final: 0.7765 (t) REVERT: s 253 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7864 (pm20) REVERT: u 6 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6926 (tm-30) REVERT: u 84 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: u 109 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6298 (tt0) REVERT: v 15 LYS cc_start: 0.8372 (mtpp) cc_final: 0.8157 (mtpm) REVERT: v 36 GLU cc_start: 0.7357 (pt0) cc_final: 0.6864 (pt0) REVERT: w 171 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8274 (tp30) outliers start: 67 outliers final: 30 residues processed: 694 average time/residue: 0.9734 time to fit residues: 790.9116 Evaluate side-chains 704 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 658 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL 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 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 130 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 35 LEU 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 92 MET 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 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 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 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 179 ILE 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 s residue 289 LEU 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 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: 0.7980 chunk 102 optimal weight: 0.3980 chunk 395 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 329 optimal weight: 4.9990 chunk 434 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 454 optimal weight: 0.9990 chunk 202 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 85 GLN W 90 ASN f 61 GLN p 53 ASN p 141 GLN r 139 GLN w 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.126753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.105101 restraints weight = 43244.849| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.02 r_work: 0.2916 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 40724 Z= 0.110 Angle : 0.528 10.029 54924 Z= 0.265 Chirality : 0.039 0.183 5933 Planarity : 0.004 0.057 6671 Dihedral : 14.613 152.065 6743 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 1.15 % Allowed : 14.31 % Favored : 84.54 % 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: 2.35 (0.12), residues: 4667 helix: 2.43 (0.09), residues: 3012 sheet: -0.41 (0.92), residues: 25 loop : -0.06 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG w 51 TYR 0.023 0.001 TYR l 422 PHE 0.032 0.001 PHE i 292 TRP 0.022 0.001 TRP l 144 HIS 0.006 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00226 (40713) covalent geometry : angle 0.52723 (54908) SS BOND : bond 0.00301 ( 8) SS BOND : angle 1.31030 ( 16) hydrogen bonds : bond 0.04521 ( 2314) hydrogen bonds : angle 4.00594 ( 6738) Misc. bond : bond 0.00029 ( 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 722 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 675 time to evaluate : 1.750 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: S 48 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8511 (mtm) REVERT: V 6 LEU cc_start: 0.8109 (mt) cc_final: 0.7372 (tp) REVERT: V 120 LEU cc_start: 0.8826 (tp) cc_final: 0.8400 (mt) REVERT: X 151 LYS cc_start: 0.8924 (tppp) cc_final: 0.8650 (tptm) REVERT: Y 90 SER cc_start: 0.8562 (m) cc_final: 0.8286 (p) REVERT: Z 61 VAL cc_start: 0.8583 (m) cc_final: 0.8241 (p) REVERT: a 72 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8267 (ttm170) REVERT: d 168 LYS cc_start: 0.8010 (tmmt) cc_final: 0.7658 (ttmm) REVERT: e 54 ARG cc_start: 0.6203 (OUTLIER) cc_final: 0.5243 (mmt90) REVERT: e 116 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: g 51 ARG cc_start: 0.8444 (mmt90) cc_final: 0.8170 (mpt180) REVERT: h 37 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: h 53 GLU cc_start: 0.8766 (tt0) cc_final: 0.8496 (tt0) REVERT: i 278 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8078 (tpt) REVERT: i 321 LYS cc_start: 0.8015 (tppt) cc_final: 0.7628 (mmmm) REVERT: j 1 MET cc_start: 0.7274 (tmt) cc_final: 0.6874 (tpt) REVERT: k 10 MET cc_start: 0.9102 (tpt) cc_final: 0.8836 (tpt) REVERT: l 387 THR cc_start: 0.8938 (t) cc_final: 0.8549 (m) REVERT: p 13 GLN cc_start: 0.8384 (tt0) cc_final: 0.7713 (mp10) REVERT: p 65 ARG cc_start: 0.8438 (mtp180) cc_final: 0.7972 (mtp-110) REVERT: p 66 GLN cc_start: 0.8452 (mt0) cc_final: 0.8164 (mp10) REVERT: p 150 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7555 (mmt180) REVERT: r 45 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7385 (mt) REVERT: s 143 GLU cc_start: 0.8560 (tp30) cc_final: 0.8340 (tm-30) REVERT: s 200 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8675 (mm) REVERT: s 251 THR cc_start: 0.8157 (m) cc_final: 0.7728 (t) REVERT: s 253 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: u 6 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: u 84 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: u 109 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6283 (tt0) REVERT: v 15 LYS cc_start: 0.8292 (mtpp) cc_final: 0.8092 (mtpm) REVERT: v 36 GLU cc_start: 0.7358 (pt0) cc_final: 0.6863 (pt0) outliers start: 47 outliers final: 27 residues processed: 696 average time/residue: 0.9111 time to fit residues: 747.2086 Evaluate side-chains 705 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 665 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 48 MET Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 44 LYS 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 130 GLU Chi-restraints excluded: chain a residue 186 THR 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 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 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 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 179 ILE 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 253 GLU Chi-restraints excluded: chain s residue 289 LEU 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: 5.9990 chunk 151 optimal weight: 4.9990 chunk 58 optimal weight: 0.1980 chunk 172 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 371 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 440 optimal weight: 2.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 85 GLN W 90 ASN Z 60 ASN b 89 HIS e 65 ASN f 61 GLN h 27 HIS p 53 ASN p 124 GLN p 141 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 = 0.3266 r_free = 0.3266 target = 0.119799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.098061 restraints weight = 43266.514| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 0.99 r_work: 0.2814 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 40724 Z= 0.198 Angle : 0.648 13.254 54924 Z= 0.329 Chirality : 0.045 0.218 5933 Planarity : 0.005 0.063 6671 Dihedral : 15.109 154.679 6743 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.34 % Favored : 96.57 % Rotamer: Outliers : 1.51 % Allowed : 14.09 % Favored : 84.40 % 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: 2.03 (0.12), residues: 4667 helix: 2.15 (0.09), residues: 3011 sheet: -0.65 (0.93), residues: 23 loop : -0.12 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG w 51 TYR 0.027 0.002 TYR w 129 PHE 0.029 0.002 PHE i 292 TRP 0.021 0.002 TRP u 86 HIS 0.009 0.001 HIS l 534 Details of bonding type rmsd covalent geometry : bond 0.00467 (40713) covalent geometry : angle 0.64754 (54908) SS BOND : bond 0.00461 ( 8) SS BOND : angle 1.80389 ( 16) hydrogen bonds : bond 0.06567 ( 2314) hydrogen bonds : angle 4.27048 ( 6738) Misc. bond : bond 0.00074 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20947.73 seconds wall clock time: 355 minutes 54.82 seconds (21354.82 seconds total)