Starting phenix.real_space_refine on Sun Feb 8 02:08:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vy1_32191/02_2026/7vy1_32191.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vy1_32191/02_2026/7vy1_32191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vy1_32191/02_2026/7vy1_32191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vy1_32191/02_2026/7vy1_32191.map" model { file = "/net/cci-nas-00/data/ceres_data/7vy1_32191/02_2026/7vy1_32191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vy1_32191/02_2026/7vy1_32191.cif" } resolution = 3.3 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 32 5.49 5 S 286 5.16 5 C 25535 2.51 5 N 6213 2.21 5 O 6833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38899 Number of models: 1 Model: "" Number of chains: 44 Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 333 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 7, 'TRANS': 32} Chain: "S" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 567 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 949 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "X" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 699 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 597 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "b" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 875 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1299 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 135} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4785 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 28, 'TRANS': 574} Chain: "m" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 951 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2394 Classifications: {'peptide': 303} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2581 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 94 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 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: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 143 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "g" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 147 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "i" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "j" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 186 Unusual residues: {'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "o" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 68 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "r" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 254 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {' UQ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1, ' UQ:plan-11': 1} Unresolved non-hydrogen planarities: 35 Chain: "u" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 78 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.59 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.59 Time building chain proxies: 8.44, per 1000 atoms: 0.22 Number of scatterers: 38899 At special positions: 0 Unit cell: (181.54, 191.208, 139.646, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 286 16.00 P 32 15.00 O 6833 8.00 N 6213 7.00 C 25535 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.6 seconds 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8814 Finding SS restraints... Secondary structure from input PDB file: 213 helices and 6 sheets defined 70.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'Q' and resid 40 through 45 Processing helix chain 'Q' and resid 46 through 49 removed outlier: 4.261A pdb=" N GLY Q 49 " --> pdb=" O GLN Q 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 46 through 49' Processing helix chain 'Q' and resid 56 through 61 removed outlier: 4.257A pdb=" N HIS Q 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 1 through 4 Processing helix chain 'S' and resid 5 through 30 Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 43 through 56 removed outlier: 4.038A pdb=" N GLY S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 4.046A pdb=" N ASP S 70 " --> pdb=" O GLU S 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 14 Processing helix chain 'U' and resid 16 through 32 removed outlier: 3.703A pdb=" N VAL U 20 " --> pdb=" O GLU U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 35 No H-bonds generated for 'chain 'U' and resid 33 through 35' Processing helix chain 'U' and resid 38 through 48 Processing helix chain 'U' and resid 78 through 84 Processing helix chain 'V' and resid 3 through 12 removed outlier: 3.888A pdb=" N ILE V 12 " --> pdb=" O LYS V 8 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 44 Processing helix chain 'V' and resid 48 through 82 Processing helix chain 'V' and resid 86 through 106 removed outlier: 4.118A pdb=" N TYR V 90 " --> pdb=" O ASP V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 132 removed outlier: 3.677A pdb=" N THR V 121 " --> pdb=" O TYR V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 98 Proline residue: W 73 - end of helix Processing helix chain 'W' and resid 120 through 125 removed outlier: 3.709A pdb=" N LEU W 124 " --> pdb=" O MET W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 129 through 143 removed outlier: 6.018A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 89 Processing helix chain 'X' and resid 111 through 127 Processing helix chain 'X' and resid 131 through 136 Processing helix chain 'X' and resid 140 through 153 Processing helix chain 'Y' and resid 51 through 76 removed outlier: 3.662A pdb=" N LEU Y 55 " --> pdb=" O THR Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 82 Processing helix chain 'Y' and resid 88 through 92 Processing helix chain 'Z' and resid 28 through 40 removed outlier: 3.966A pdb=" N VAL Z 32 " --> pdb=" O PRO Z 28 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 53 removed outlier: 3.700A pdb=" N GLU Z 49 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 59 removed outlier: 4.000A pdb=" N ASN Z 59 " --> pdb=" O GLY Z 56 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 68 Processing helix chain 'Z' and resid 70 through 90 Processing helix chain 'a' and resid 61 through 93 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 115 through 126 Processing helix chain 'a' and resid 128 through 164 removed outlier: 4.067A pdb=" N ASN a 132 " --> pdb=" O GLY a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 179 removed outlier: 3.840A pdb=" N LEU a 178 " --> pdb=" O ASP a 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 26 Processing helix chain 'b' and resid 65 through 74 removed outlier: 3.520A pdb=" N VAL b 72 " --> pdb=" O SER b 68 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 89 Processing helix chain 'c' and resid 33 through 37 Processing helix chain 'c' and resid 44 through 55 Processing helix chain 'c' and resid 58 through 62 Processing helix chain 'c' and resid 108 through 112 Processing helix chain 'c' and resid 125 through 150 Processing helix chain 'd' and resid 28 through 41 removed outlier: 3.891A pdb=" N TYR d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 58 removed outlier: 3.589A pdb=" N LYS d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 77 removed outlier: 3.553A pdb=" N GLU d 76 " --> pdb=" O ASP d 73 " (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 176 Processing helix chain 'e' and resid 79 through 95 Processing helix chain 'e' and resid 97 through 108 removed outlier: 3.915A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 114 through 132 removed outlier: 3.577A pdb=" N ALA e 118 " --> pdb=" O MET e 114 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 73 Processing helix chain 'g' and resid 3 through 7 removed outlier: 4.230A pdb=" N GLY g 6 " --> pdb=" O MET g 3 " (cutoff:3.500A) Processing helix chain 'g' and resid 17 through 23 removed outlier: 3.541A pdb=" N LEU g 23 " --> pdb=" O ALA g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 30 through 51 Processing helix chain 'g' and resid 59 through 99 Processing helix chain 'g' and resid 110 through 114 removed outlier: 3.567A pdb=" N ILE g 114 " --> pdb=" O TYR g 111 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 11 Processing helix chain 'h' and resid 25 through 29 Processing helix chain 'h' and resid 33 through 44 Processing helix chain 'h' and resid 48 through 56 Processing helix chain 'h' and resid 56 through 69 Processing helix chain 'h' and resid 69 through 90 Processing helix chain 'h' and resid 95 through 100 removed outlier: 3.745A pdb=" N GLY h 100 " --> pdb=" O HIS h 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 23 Processing helix chain 'i' and resid 25 through 45 removed outlier: 3.580A pdb=" N ILE i 41 " --> pdb=" O LEU i 37 " (cutoff:3.500A) Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 49 through 81 Processing helix chain 'i' and resid 91 through 107 Processing helix chain 'i' and resid 113 through 122 removed outlier: 4.277A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 123 through 133 Processing helix chain 'i' and resid 135 through 145 Processing helix chain 'i' and resid 150 through 172 removed outlier: 3.872A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN i 172 " --> pdb=" O GLY i 168 " (cutoff:3.500A) Processing helix chain 'i' and resid 174 through 192 removed outlier: 3.598A pdb=" N ALA i 192 " --> pdb=" O GLY i 188 " (cutoff:3.500A) Processing helix chain 'i' and resid 197 through 222 removed outlier: 3.640A pdb=" N THR i 201 " --> pdb=" O ASN i 197 " (cutoff:3.500A) Processing helix chain 'i' and resid 226 through 232 Processing helix chain 'i' and resid 233 through 236 Processing helix chain 'i' and resid 237 through 252 removed outlier: 3.550A pdb=" N THR i 241 " --> pdb=" O MET i 237 " (cutoff:3.500A) Processing helix chain 'i' and resid 259 through 273 removed outlier: 4.514A pdb=" N LYS i 263 " --> pdb=" O GLY i 259 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN i 273 " --> pdb=" O GLU i 269 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 301 removed outlier: 3.542A pdb=" N THR i 280 " --> pdb=" O ILE i 276 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 315 removed outlier: 3.893A pdb=" N LYS i 314 " --> pdb=" O ASN i 310 " (cutoff:3.500A) Processing helix chain 'i' and resid 325 through 335 Processing helix chain 'i' and resid 336 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 24 Processing helix chain 'j' and resid 25 through 27 No H-bonds generated for 'chain 'j' and resid 25 through 27' Processing helix chain 'j' and resid 52 through 73 removed outlier: 4.029A pdb=" N PHE j 56 " --> pdb=" O SER j 52 " (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 22 removed outlier: 3.599A pdb=" N MET k 6 " --> pdb=" O PRO k 2 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR k 22 " --> pdb=" O GLY k 18 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 51 removed outlier: 3.677A pdb=" N SER k 29 " --> pdb=" O HIS k 25 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 56 Processing helix chain 'k' and resid 57 through 86 removed outlier: 4.627A pdb=" N ILE k 61 " --> pdb=" O ASN k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 89 through 93 Processing helix chain 'l' and resid 2 through 15 removed outlier: 4.486A pdb=" N SER l 6 " --> pdb=" O ASN l 2 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 22 Processing helix chain 'l' and resid 23 through 24 No H-bonds generated for 'chain 'l' and resid 23 through 24' Processing helix chain 'l' and resid 25 through 29 Processing helix chain 'l' and resid 31 through 58 removed outlier: 4.618A 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: 3.869A 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 removed outlier: 3.503A pdb=" N GLY l 148 " --> pdb=" O TRP l 144 " (cutoff:3.500A) Processing helix chain 'l' and resid 161 through 194 removed outlier: 3.614A pdb=" N ASN l 165 " --> pdb=" O ARG l 161 " (cutoff:3.500A) removed outlier: 3.943A 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: 4.188A pdb=" N LEU l 213 " --> pdb=" O PRO l 209 " (cutoff:3.500A) Processing helix chain 'l' and resid 226 through 230 removed outlier: 3.775A pdb=" N HIS l 230 " --> pdb=" O PHE l 227 " (cutoff:3.500A) Processing helix chain 'l' and resid 231 through 236 Processing helix chain 'l' and resid 237 through 239 No H-bonds generated for 'chain 'l' and resid 237 through 239' Processing helix chain 'l' and resid 240 through 247 Processing helix chain 'l' and resid 254 through 263 Processing helix chain 'l' and resid 263 through 268 Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.253A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 297 through 319 Processing helix chain 'l' and resid 321 through 350 removed outlier: 3.690A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 355 through 359 Processing helix chain 'l' and resid 366 through 382 Processing helix chain 'l' and resid 386 through 401 removed outlier: 3.528A pdb=" N TYR l 390 " --> pdb=" O LEU l 386 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER l 391 " --> pdb=" O THR l 387 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 405 through 432 removed outlier: 3.581A pdb=" N LEU l 432 " --> pdb=" O PHE l 428 " (cutoff:3.500A) Processing helix chain 'l' and resid 447 through 471 removed outlier: 3.594A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 483 through 488 Processing helix chain 'l' and resid 488 through 507 removed outlier: 3.605A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) Processing helix chain 'l' and resid 508 through 510 No H-bonds generated for 'chain 'l' and resid 508 through 510' Processing helix chain 'l' and resid 517 through 525 Processing helix chain 'l' and resid 528 through 534 Processing helix chain 'l' and resid 535 through 548 removed outlier: 3.671A pdb=" N TYR l 539 " --> pdb=" O ARG l 535 " (cutoff:3.500A) Processing helix chain 'l' and resid 556 through 562 removed outlier: 3.808A 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: 3.514A pdb=" N TYR l 587 " --> pdb=" O LEU l 583 " (cutoff:3.500A) Processing helix chain 'm' and resid 4 through 22 removed outlier: 3.534A pdb=" N SER m 22 " --> pdb=" O VAL m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 48 removed outlier: 3.584A pdb=" N GLY m 29 " --> pdb=" O SER m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 75 removed outlier: 4.073A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 137 through 145 Processing helix chain 'm' and resid 150 through 174 removed outlier: 4.442A pdb=" N GLY m 174 " --> pdb=" O GLU m 170 " (cutoff:3.500A) Processing helix chain 'n' and resid 7 through 12 Processing helix chain 'n' and resid 15 through 33 Processing helix chain 'o' and resid 26 through 52 Processing helix chain 'o' and resid 62 through 74 Processing helix chain 'o' and resid 83 through 119 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 11 through 31 Processing helix chain 'p' and resid 33 through 50 Processing helix chain 'p' and resid 56 through 63 removed outlier: 3.512A pdb=" N ALA p 60 " --> pdb=" O ASP p 56 " (cutoff:3.500A) Processing helix chain 'p' and resid 65 through 74 Processing helix chain 'p' and resid 92 through 97 removed outlier: 4.373A pdb=" N CYS p 96 " --> pdb=" O ARG p 93 " (cutoff:3.500A) Processing helix chain 'p' and resid 100 through 107 removed outlier: 3.537A pdb=" N TRP p 107 " --> pdb=" O LEU p 104 " (cutoff:3.500A) Processing helix chain 'p' and resid 108 through 114 removed outlier: 3.990A pdb=" N MET p 114 " --> pdb=" O SER p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 115 through 144 removed outlier: 3.539A pdb=" N PHE p 119 " --> pdb=" O TYR p 115 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS p 138 " --> pdb=" O GLU p 134 " (cutoff:3.500A) Processing helix chain 'p' and resid 167 through 172 Processing helix chain 'r' and resid 2 through 17 Proline residue: r 7 - end of helix removed outlier: 4.091A 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: 3.539A 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: 4.080A pdb=" N LEU r 65 " --> pdb=" O LEU r 61 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 88 through 112 removed outlier: 3.850A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA r 112 " --> pdb=" O MET r 108 " (cutoff:3.500A) Processing helix chain 'r' and resid 114 through 125 Processing helix chain 'r' and resid 126 through 136 Processing helix chain 'r' and resid 141 through 172 removed outlier: 3.569A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY r 156 " --> pdb=" O TYR r 152 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.788A pdb=" N VAL r 162 " --> pdb=" O LEU r 158 " (cutoff:3.500A) Processing helix chain 'r' and resid 175 through 182 Processing helix chain 'r' and resid 189 through 207 removed outlier: 4.021A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 223 removed outlier: 4.152A 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: 4.131A 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: 4.341A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG r 278 " --> pdb=" O SER r 274 " (cutoff:3.500A) Processing helix chain 'r' and resid 281 through 304 removed outlier: 3.545A pdb=" N GLN r 304 " --> pdb=" O ALA r 300 " (cutoff:3.500A) Processing helix chain 'r' and resid 305 through 338 removed outlier: 3.643A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 347 through 352 removed outlier: 4.242A 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: 4.240A pdb=" N LEU r 395 " --> pdb=" O ILE r 391 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR r 414 " --> pdb=" O MET r 410 " (cutoff:3.500A) Processing helix chain 'r' and resid 430 through 448 removed outlier: 3.561A pdb=" N ASN r 434 " --> pdb=" O PHE r 430 " (cutoff:3.500A) Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 449 through 455 removed outlier: 6.413A pdb=" N LYS r 452 " --> pdb=" O LEU r 449 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU r 455 " --> pdb=" O LYS r 452 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 4.030A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 46 through 57 Processing helix chain 's' and resid 67 through 85 Proline residue: s 75 - end of helix Processing helix chain 's' and resid 100 through 112 Processing helix chain 's' and resid 112 through 123 removed outlier: 4.209A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 125 through 155 removed outlier: 3.854A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 169 removed outlier: 3.811A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) Processing helix chain 's' and resid 173 through 178 removed outlier: 4.076A pdb=" N THR s 177 " --> pdb=" O TRP s 173 " (cutoff:3.500A) Processing helix chain 's' and resid 178 through 193 removed outlier: 3.575A pdb=" N ALA s 182 " --> pdb=" O SER s 178 " (cutoff:3.500A) Processing helix chain 's' and resid 218 through 243 Processing helix chain 's' and resid 251 through 277 removed outlier: 4.511A pdb=" N TYR s 255 " --> pdb=" O THR s 251 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR s 277 " --> pdb=" O ILE s 273 " (cutoff:3.500A) Processing helix chain 's' and resid 281 through 312 removed outlier: 4.978A pdb=" N LEU s 294 " --> pdb=" O TRP s 290 " (cutoff:3.500A) Proline residue: s 295 - end of helix Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 21 through 28 Processing helix chain 'u' and resid 28 through 36 Processing helix chain 'u' and resid 36 through 51 removed outlier: 3.611A pdb=" N ASN u 40 " --> pdb=" O CYS u 36 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 55 Processing helix chain 'u' and resid 56 through 78 Processing helix chain 'u' and resid 78 through 92 removed outlier: 3.792A pdb=" N SER u 92 " --> pdb=" O CYS u 88 " (cutoff:3.500A) Processing helix chain 'u' and resid 100 through 115 Processing helix chain 'v' and resid 3 through 11 Processing helix chain 'v' and resid 12 through 16 removed outlier: 3.683A pdb=" N GLU v 16 " --> pdb=" O ALA v 13 " (cutoff:3.500A) Processing helix chain 'v' and resid 26 through 30 removed outlier: 4.041A pdb=" N GLY v 30 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing helix chain 'v' and resid 42 through 50 Processing helix chain 'v' and resid 59 through 73 removed outlier: 3.585A pdb=" N LEU v 63 " --> pdb=" O CYS v 59 " (cutoff:3.500A) Processing helix chain 'v' and resid 81 through 125 Processing helix chain 'w' and resid 39 through 46 Processing helix chain 'w' and resid 69 through 82 Processing helix chain 'w' and resid 92 through 98 removed outlier: 3.761A pdb=" N SER w 96 " --> pdb=" O HIS w 92 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR w 97 " --> pdb=" O TYR w 93 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR w 98 " --> pdb=" O ALA w 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 92 through 98' Processing helix chain 'w' and resid 113 through 120 Processing helix chain 'w' and resid 126 through 154 removed outlier: 3.529A pdb=" N ARG w 130 " --> pdb=" O GLY w 126 " (cutoff:3.500A) Processing helix chain 'w' and resid 166 through 176 removed outlier: 3.910A pdb=" N LEU w 170 " --> pdb=" O ASP w 166 " (cutoff:3.500A) Processing helix chain 'w' and resid 180 through 196 removed outlier: 3.554A pdb=" N VAL w 184 " --> pdb=" O ARG w 180 " (cutoff:3.500A) Processing helix chain 'w' and resid 210 through 222 removed outlier: 3.619A pdb=" N GLY w 222 " --> pdb=" O ILE w 218 " (cutoff:3.500A) Processing helix chain 'w' and resid 225 through 229 Processing helix chain 'w' and resid 230 through 244 removed outlier: 3.548A pdb=" N THR w 244 " --> pdb=" O ALA w 240 " (cutoff:3.500A) Processing helix chain 'w' and resid 244 through 251 Processing helix chain 'w' and resid 265 through 276 removed outlier: 3.665A pdb=" N VAL w 269 " --> pdb=" O ASP w 265 " (cutoff:3.500A) Processing helix chain 'w' and resid 287 through 299 removed outlier: 3.510A pdb=" N GLN w 299 " --> pdb=" O ARG w 295 " (cutoff:3.500A) Processing helix chain 'w' and resid 300 through 305 removed outlier: 3.766A pdb=" N VAL w 304 " --> pdb=" O ASN w 300 " (cutoff:3.500A) Processing helix chain 'w' and resid 306 through 310 removed outlier: 3.971A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE w 310 " --> pdb=" O TYR w 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 310' Processing helix chain 'w' and resid 320 through 333 Processing helix chain 'w' and resid 351 through 355 Processing sheet with id=AA1, first strand: chain 'U' and resid 57 through 58 removed outlier: 6.626A 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: 6.123A 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: 5.366A pdb=" N SER l 64 " --> pdb=" O PHE l 80 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE l 80 " --> pdb=" O SER l 64 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TRP l 66 " --> pdb=" O LEU l 78 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU l 76 " --> pdb=" O TRP l 68 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR l 70 " --> pdb=" O VAL l 74 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL l 74 " --> pdb=" O THR l 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'i' and resid 307 through 308 Processing sheet with id=AA5, first strand: chain 'r' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'w' and resid 84 through 86 2286 hydrogen bonds defined for protein. 6678 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: 7.24 Time building geometry restraints manager: 4.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5874 1.31 - 1.44: 10823 1.44 - 1.56: 22522 1.56 - 1.69: 164 1.69 - 1.82: 517 Bond restraints: 39900 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C4' ADP w 401 " pdb=" O4' ADP w 401 " ideal model delta sigma weight residual 1.426 1.617 -0.191 2.00e-02 2.50e+03 9.08e+01 bond pdb=" CA7 CDL u 201 " pdb=" OA8 CDL u 201 " ideal model delta sigma weight residual 1.334 1.430 -0.096 1.10e-02 8.26e+03 7.68e+01 bond pdb=" CA7 CDL V 201 " pdb=" OA8 CDL V 201 " ideal model delta sigma weight residual 1.334 1.430 -0.096 1.10e-02 8.26e+03 7.56e+01 bond pdb=" CA7 CDL i 401 " pdb=" OA8 CDL i 401 " ideal model delta sigma weight residual 1.334 1.429 -0.095 1.10e-02 8.26e+03 7.50e+01 ... (remaining 39895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 53287 3.47 - 6.93: 475 6.93 - 10.40: 96 10.40 - 13.86: 12 13.86 - 17.33: 8 Bond angle restraints: 53878 Sorted by residual: angle pdb=" C ASP e 143 " pdb=" N PRO e 144 " pdb=" CA PRO e 144 " ideal model delta sigma weight residual 119.05 127.31 -8.26 1.11e+00 8.12e-01 5.54e+01 angle pdb=" C11 CDL a 201 " pdb=" CA5 CDL a 201 " pdb=" OA6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.78 -9.45 1.32e+00 5.72e-01 5.11e+01 angle pdb=" C51 CDL r 504 " pdb=" CB5 CDL r 504 " pdb=" OB6 CDL r 504 " ideal model delta sigma weight residual 111.33 120.59 -9.26 1.32e+00 5.72e-01 4.91e+01 angle pdb=" C51 CDL u 201 " pdb=" CB5 CDL u 201 " pdb=" OB6 CDL u 201 " ideal model delta sigma weight residual 111.33 120.43 -9.10 1.32e+00 5.72e-01 4.74e+01 angle pdb=" C11 CDL i 401 " pdb=" CA5 CDL i 401 " pdb=" OA6 CDL i 401 " ideal model delta sigma weight residual 111.33 120.38 -9.05 1.32e+00 5.72e-01 4.69e+01 ... (remaining 53873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 23164 35.10 - 70.20: 1046 70.20 - 105.30: 77 105.30 - 140.40: 20 140.40 - 175.50: 11 Dihedral angle restraints: 24318 sinusoidal: 10680 harmonic: 13638 Sorted by residual: dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual 300.00 124.50 175.50 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C32 PEE W 201 " pdb=" C30 PEE W 201 " pdb=" C31 PEE W 201 " pdb=" O3 PEE W 201 " ideal model delta sinusoidal sigma weight residual 161.16 -2.62 163.78 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C2 PLX r 502 " pdb=" O1 PLX r 502 " pdb=" P1 PLX r 502 " pdb=" O3 PLX r 502 " ideal model delta sinusoidal sigma weight residual 310.56 150.32 160.24 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 24315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 5393 0.077 - 0.154: 424 0.154 - 0.231: 19 0.231 - 0.308: 2 0.308 - 0.385: 4 Chirality restraints: 5842 Sorted by residual: chirality pdb=" C6 PLX a 202 " pdb=" C7 PLX a 202 " pdb=" O6 PLX a 202 " pdb=" O7 PLX a 202 " both_signs ideal model delta sigma weight residual False 2.01 2.40 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" C6 PLX g 201 " pdb=" C7 PLX g 201 " pdb=" O6 PLX g 201 " pdb=" O7 PLX g 201 " both_signs ideal model delta sigma weight residual False 2.01 2.34 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C6 PLX r 503 " pdb=" C7 PLX r 503 " pdb=" O6 PLX r 503 " pdb=" O7 PLX r 503 " both_signs ideal model delta sigma weight residual False 2.01 2.33 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 5839 not shown) Planarity restraints: 6572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP v 18 " 0.046 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO v 19 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO v 19 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO v 19 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN l 320 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C ASN l 320 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN l 320 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN l 321 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP d 38 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ASP d 38 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP d 38 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU d 39 " 0.013 2.00e-02 2.50e+03 ... (remaining 6569 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 407 2.63 - 3.20: 34550 3.20 - 3.76: 60294 3.76 - 4.33: 82309 4.33 - 4.90: 140229 Nonbonded interactions: 317789 Sorted by model distance: nonbonded pdb=" OE2 GLU e 151 " pdb=" OD1 ASP e 152 " model vdw 2.061 3.040 nonbonded pdb=" O ARG w 261 " pdb=" NH1 ARG w 261 " model vdw 2.165 3.120 nonbonded pdb=" OG SER w 123 " pdb=" OD1 ASP w 125 " model vdw 2.212 3.040 nonbonded pdb=" OE1 GLU p 101 " pdb=" NH1 ARG p 122 " model vdw 2.216 3.120 nonbonded pdb=" OH TYR a 133 " pdb=" OE1 GLU d 87 " model vdw 2.218 3.040 ... (remaining 317784 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=0.59 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 33.800 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.226 39907 Z= 0.413 Angle : 0.846 17.326 53890 Z= 0.421 Chirality : 0.044 0.385 5842 Planarity : 0.004 0.071 6572 Dihedral : 19.136 175.498 15486 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.36 % Favored : 95.60 % Rotamer: Outliers : 0.20 % Allowed : 13.15 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.13), residues: 4586 helix: 2.09 (0.10), residues: 2953 sheet: 0.92 (1.10), residues: 24 loop : -0.58 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG n 30 TYR 0.030 0.001 TYR w 129 PHE 0.030 0.001 PHE i 292 TRP 0.021 0.001 TRP u 86 HIS 0.006 0.001 HIS v 61 Details of bonding type rmsd covalent geometry : bond 0.00743 (39900) covalent geometry : angle 0.84568 (53878) SS BOND : bond 0.00321 ( 6) SS BOND : angle 1.77050 ( 12) hydrogen bonds : bond 0.12621 ( 2286) hydrogen bonds : angle 5.04232 ( 6678) Misc. bond : bond 0.19944 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 714 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: W 130 ASN cc_start: 0.8420 (m-40) cc_final: 0.8163 (t0) REVERT: a 78 THR cc_start: 0.8508 (m) cc_final: 0.8037 (m) REVERT: h 65 GLU cc_start: 0.8948 (tp30) cc_final: 0.8667 (tp30) REVERT: i 284 MET cc_start: 0.8961 (mmm) cc_final: 0.8619 (mmt) REVERT: o 117 GLN cc_start: 0.8272 (mm-40) cc_final: 0.8041 (mp10) REVERT: r 1 MET cc_start: 0.8910 (ttm) cc_final: 0.8695 (ttt) REVERT: u 90 ASP cc_start: 0.9075 (t70) cc_final: 0.8721 (t0) REVERT: v 38 GLU cc_start: 0.8452 (pm20) cc_final: 0.8231 (pm20) outliers start: 8 outliers final: 5 residues processed: 717 average time/residue: 0.2369 time to fit residues: 279.7863 Evaluate side-chains 704 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 699 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain w residue 285 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 0.3980 chunk 424 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 83 GLN d 124 ASN j 83 ASN m 175 ASN r 192 ASN s 235 ASN v 47 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.075120 restraints weight = 62249.950| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.83 r_work: 0.2686 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 39907 Z= 0.180 Angle : 0.591 10.173 53890 Z= 0.294 Chirality : 0.042 0.181 5842 Planarity : 0.004 0.054 6572 Dihedral : 17.107 178.234 6356 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 1.70 % Allowed : 12.61 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.13), residues: 4586 helix: 2.20 (0.10), residues: 2985 sheet: 1.01 (1.10), residues: 24 loop : -0.52 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG n 30 TYR 0.025 0.001 TYR w 129 PHE 0.030 0.001 PHE i 292 TRP 0.021 0.001 TRP u 86 HIS 0.006 0.001 HIS v 61 Details of bonding type rmsd covalent geometry : bond 0.00433 (39900) covalent geometry : angle 0.59041 (53878) SS BOND : bond 0.00321 ( 6) SS BOND : angle 1.62883 ( 12) hydrogen bonds : bond 0.05259 ( 2286) hydrogen bonds : angle 4.17525 ( 6678) Misc. bond : bond 0.00353 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 714 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 71 PHE cc_start: 0.8649 (t80) cc_final: 0.8421 (t80) REVERT: a 78 THR cc_start: 0.8585 (m) cc_final: 0.8036 (m) REVERT: a 152 LYS cc_start: 0.8989 (ttmm) cc_final: 0.8765 (ttmt) REVERT: i 11 MET cc_start: 0.8687 (mmp) cc_final: 0.8376 (mmm) REVERT: i 284 MET cc_start: 0.8906 (mmm) cc_final: 0.8694 (mmt) REVERT: j 108 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7248 (mp10) REVERT: k 91 GLN cc_start: 0.8447 (pm20) cc_final: 0.8224 (pm20) REVERT: l 357 ARG cc_start: 0.9017 (mpp80) cc_final: 0.8545 (mtt90) REVERT: m 34 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8855 (mp) REVERT: m 135 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.7684 (t80) REVERT: p 123 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8241 (mp0) REVERT: r 1 MET cc_start: 0.8825 (ttm) cc_final: 0.8270 (tpt) REVERT: u 90 ASP cc_start: 0.9054 (t70) cc_final: 0.8655 (t0) REVERT: v 38 GLU cc_start: 0.8683 (pm20) cc_final: 0.8454 (pm20) REVERT: w 120 ASP cc_start: 0.8170 (t0) cc_final: 0.7664 (t0) REVERT: w 246 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8287 (mm) REVERT: w 312 VAL cc_start: 0.9264 (OUTLIER) cc_final: 0.9051 (p) outliers start: 69 outliers final: 38 residues processed: 754 average time/residue: 0.2369 time to fit residues: 294.6618 Evaluate side-chains 739 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 696 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain j residue 108 GLN Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain m residue 34 ILE Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 50 GLU Chi-restraints excluded: chain p residue 61 THR Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 125 THR Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain w residue 246 LEU Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 66 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 397 optimal weight: 0.9980 chunk 241 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 344 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 340 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 86 ASN s 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.096136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.076289 restraints weight = 61802.662| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.82 r_work: 0.2706 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39907 Z= 0.140 Angle : 0.552 9.403 53890 Z= 0.274 Chirality : 0.040 0.181 5842 Planarity : 0.004 0.056 6572 Dihedral : 15.913 169.305 6347 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.88 % Favored : 96.10 % Rotamer: Outliers : 2.06 % Allowed : 13.42 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.13), residues: 4586 helix: 2.28 (0.10), residues: 2989 sheet: 0.89 (1.09), residues: 24 loop : -0.52 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG n 30 TYR 0.021 0.001 TYR l 422 PHE 0.028 0.001 PHE i 292 TRP 0.020 0.001 TRP u 86 HIS 0.004 0.001 HIS p 26 Details of bonding type rmsd covalent geometry : bond 0.00328 (39900) covalent geometry : angle 0.55198 (53878) SS BOND : bond 0.00307 ( 6) SS BOND : angle 1.52731 ( 12) hydrogen bonds : bond 0.04739 ( 2286) hydrogen bonds : angle 4.00889 ( 6678) Misc. bond : bond 0.00066 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 731 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 53 ARG cc_start: 0.9001 (mtp180) cc_final: 0.8693 (mtm-85) REVERT: Y 93 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8826 (p) REVERT: Y 96 GLU cc_start: 0.8728 (pm20) cc_final: 0.8227 (pm20) REVERT: Z 71 PHE cc_start: 0.8641 (t80) cc_final: 0.8406 (t80) REVERT: a 78 THR cc_start: 0.8461 (m) cc_final: 0.7966 (m) REVERT: a 152 LYS cc_start: 0.8995 (ttmm) cc_final: 0.8770 (ttmt) REVERT: c 84 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8487 (tm-30) REVERT: e 77 ASP cc_start: 0.8905 (t0) cc_final: 0.8553 (t0) REVERT: i 11 MET cc_start: 0.8678 (mmp) cc_final: 0.8349 (mmm) REVERT: j 68 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: j 108 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: k 59 MET cc_start: 0.8485 (tmm) cc_final: 0.8269 (ttp) REVERT: l 357 ARG cc_start: 0.8980 (mpp80) cc_final: 0.8739 (mtt90) REVERT: m 34 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8832 (mp) REVERT: m 135 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.7656 (t80) REVERT: m 169 MET cc_start: 0.9082 (mmm) cc_final: 0.8748 (mmm) REVERT: p 123 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8236 (mp0) REVERT: p 131 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: r 1 MET cc_start: 0.8630 (ttm) cc_final: 0.8425 (tpt) REVERT: u 90 ASP cc_start: 0.9068 (t70) cc_final: 0.8626 (t0) REVERT: v 38 GLU cc_start: 0.8658 (pm20) cc_final: 0.8442 (pm20) REVERT: w 120 ASP cc_start: 0.8149 (t0) cc_final: 0.7647 (t0) REVERT: w 246 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8245 (mm) REVERT: w 250 SER cc_start: 0.8990 (m) cc_final: 0.8788 (p) REVERT: w 303 GLU cc_start: 0.8107 (tp30) cc_final: 0.7891 (tp30) REVERT: w 312 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.9064 (p) outliers start: 84 outliers final: 50 residues processed: 776 average time/residue: 0.2435 time to fit residues: 310.2552 Evaluate side-chains 769 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 711 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 152 LYS Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain h residue 47 ILE Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain j residue 108 GLN Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 82 SER Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 34 ILE Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 131 GLU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 125 THR Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 246 LEU Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 217 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 111 optimal weight: 0.0770 chunk 63 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 304 optimal weight: 3.9990 chunk 340 optimal weight: 0.6980 chunk 259 optimal weight: 0.9990 chunk 275 optimal weight: 3.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 83 ASN a 90 ASN g 18 ASN i 322 GLN l 447 ASN l 541 ASN s 235 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.095989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.076089 restraints weight = 61737.988| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.84 r_work: 0.2702 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 39907 Z= 0.148 Angle : 0.554 9.359 53890 Z= 0.274 Chirality : 0.040 0.181 5842 Planarity : 0.004 0.056 6572 Dihedral : 15.049 159.432 6347 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.86 % Favored : 96.12 % Rotamer: Outliers : 2.43 % Allowed : 14.13 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.13), residues: 4586 helix: 2.30 (0.10), residues: 2985 sheet: 0.64 (1.05), residues: 24 loop : -0.53 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG n 30 TYR 0.027 0.001 TYR w 129 PHE 0.028 0.001 PHE i 292 TRP 0.020 0.001 TRP u 86 HIS 0.004 0.001 HIS p 26 Details of bonding type rmsd covalent geometry : bond 0.00354 (39900) covalent geometry : angle 0.55396 (53878) SS BOND : bond 0.00302 ( 6) SS BOND : angle 1.50489 ( 12) hydrogen bonds : bond 0.04669 ( 2286) hydrogen bonds : angle 3.95191 ( 6678) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 732 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 134 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8543 (mp) REVERT: Y 96 GLU cc_start: 0.8819 (pm20) cc_final: 0.8100 (pm20) REVERT: Z 71 PHE cc_start: 0.8664 (t80) cc_final: 0.8423 (t80) REVERT: a 78 THR cc_start: 0.8498 (m) cc_final: 0.8009 (m) REVERT: a 152 LYS cc_start: 0.8988 (ttmm) cc_final: 0.8752 (ttmt) REVERT: c 84 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8488 (tm-30) REVERT: e 77 ASP cc_start: 0.8954 (t0) cc_final: 0.8568 (t0) REVERT: e 87 MET cc_start: 0.9119 (tmm) cc_final: 0.8864 (tmm) REVERT: i 11 MET cc_start: 0.8697 (mmp) cc_final: 0.8392 (mmm) REVERT: j 68 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: j 108 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.7175 (mp10) REVERT: k 82 SER cc_start: 0.9031 (OUTLIER) cc_final: 0.8791 (t) REVERT: k 91 GLN cc_start: 0.8507 (pm20) cc_final: 0.8082 (pm20) REVERT: l 357 ARG cc_start: 0.8947 (mpp80) cc_final: 0.8627 (mtt90) REVERT: l 504 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8773 (tt) REVERT: m 34 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8831 (mp) REVERT: m 135 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.7656 (t80) REVERT: m 169 MET cc_start: 0.9101 (mmm) cc_final: 0.8738 (mmm) REVERT: o 25 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7429 (pt) REVERT: p 123 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8291 (mp0) REVERT: s 287 HIS cc_start: 0.8358 (m-70) cc_final: 0.7494 (t-90) REVERT: u 90 ASP cc_start: 0.9070 (t70) cc_final: 0.8630 (t0) REVERT: v 38 GLU cc_start: 0.8673 (pm20) cc_final: 0.8457 (pm20) REVERT: v 88 ASP cc_start: 0.9265 (m-30) cc_final: 0.8956 (m-30) REVERT: v 101 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8192 (mm-30) REVERT: w 76 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8362 (mt-10) REVERT: w 120 ASP cc_start: 0.8143 (t0) cc_final: 0.7656 (t0) REVERT: w 246 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8348 (mm) REVERT: w 250 SER cc_start: 0.9040 (m) cc_final: 0.8821 (p) REVERT: w 303 GLU cc_start: 0.8142 (tp30) cc_final: 0.7821 (tp30) REVERT: w 312 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.9073 (m) outliers start: 99 outliers final: 66 residues processed: 787 average time/residue: 0.2412 time to fit residues: 311.9181 Evaluate side-chains 790 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 714 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 152 LYS Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain h residue 47 ILE Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain j residue 108 GLN Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 82 SER Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 102 GLU Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 545 SER Chi-restraints excluded: chain m residue 34 ILE Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 50 GLU Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 125 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 94 LEU Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 246 LEU Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 257 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 344 optimal weight: 0.9990 chunk 417 optimal weight: 2.9990 chunk 342 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 294 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 83 ASN g 18 ASN i 322 GLN l 270 ASN l 541 ASN ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 235 ASN w 300 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.097194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.077266 restraints weight = 61479.727| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.84 r_work: 0.2724 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39907 Z= 0.125 Angle : 0.542 9.242 53890 Z= 0.268 Chirality : 0.040 0.180 5842 Planarity : 0.004 0.055 6572 Dihedral : 14.305 160.709 6347 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.75 % Favored : 96.23 % Rotamer: Outliers : 2.53 % Allowed : 14.72 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.13), residues: 4586 helix: 2.38 (0.09), residues: 2986 sheet: 0.56 (1.08), residues: 24 loop : -0.47 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG l 176 TYR 0.025 0.001 TYR w 129 PHE 0.029 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.004 0.001 HIS p 26 Details of bonding type rmsd covalent geometry : bond 0.00287 (39900) covalent geometry : angle 0.54132 (53878) SS BOND : bond 0.00376 ( 6) SS BOND : angle 1.78925 ( 12) hydrogen bonds : bond 0.04371 ( 2286) hydrogen bonds : angle 3.87787 ( 6678) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 747 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 130 ASN cc_start: 0.8417 (m-40) cc_final: 0.7824 (t0) REVERT: W 134 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8522 (mp) REVERT: X 124 ASP cc_start: 0.8729 (m-30) cc_final: 0.8470 (m-30) REVERT: Y 96 GLU cc_start: 0.8766 (pm20) cc_final: 0.8288 (pm20) REVERT: Z 71 PHE cc_start: 0.8648 (t80) cc_final: 0.8403 (t80) REVERT: a 78 THR cc_start: 0.8365 (m) cc_final: 0.7883 (m) REVERT: c 84 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8442 (tm-30) REVERT: e 77 ASP cc_start: 0.8954 (t0) cc_final: 0.8564 (t0) REVERT: e 87 MET cc_start: 0.9040 (tmm) cc_final: 0.8799 (tmm) REVERT: e 146 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8713 (mttm) REVERT: i 11 MET cc_start: 0.8721 (mmp) cc_final: 0.8418 (mmm) REVERT: j 68 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: j 108 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7131 (mp10) REVERT: k 91 GLN cc_start: 0.8483 (pm20) cc_final: 0.8008 (pm20) REVERT: l 504 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8778 (tt) REVERT: m 1 MET cc_start: 0.4359 (tmm) cc_final: 0.3901 (tmm) REVERT: m 34 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8769 (mp) REVERT: m 135 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.7756 (t80) REVERT: m 173 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.8153 (ttm-80) REVERT: o 25 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7499 (pt) REVERT: p 123 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8295 (mp0) REVERT: r 324 SER cc_start: 0.9436 (t) cc_final: 0.9217 (t) REVERT: s 287 HIS cc_start: 0.8330 (m-70) cc_final: 0.7533 (t70) REVERT: u 90 ASP cc_start: 0.8955 (t70) cc_final: 0.8487 (t0) REVERT: v 38 GLU cc_start: 0.8654 (pm20) cc_final: 0.8451 (pm20) REVERT: v 101 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8260 (mm-30) REVERT: w 76 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8360 (mt-10) REVERT: w 120 ASP cc_start: 0.8044 (t0) cc_final: 0.7612 (t0) REVERT: w 246 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8301 (mm) REVERT: w 303 GLU cc_start: 0.8128 (tp30) cc_final: 0.7762 (tp30) REVERT: w 312 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.9054 (m) outliers start: 103 outliers final: 66 residues processed: 804 average time/residue: 0.2369 time to fit residues: 314.7730 Evaluate side-chains 790 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 715 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain h residue 47 ILE Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain i residue 254 LEU Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain j residue 108 GLN Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 545 SER Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 34 ILE Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 50 GLU Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 125 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 214 LEU Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 288 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 94 LEU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 246 LEU Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 316 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 428 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 362 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 339 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 445 optimal weight: 0.6980 chunk 88 optimal weight: 0.0170 chunk 56 optimal weight: 3.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 83 ASN g 18 ASN i 322 GLN l 541 ASN ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 235 ASN ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.078461 restraints weight = 61197.769| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.83 r_work: 0.2729 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39907 Z= 0.115 Angle : 0.540 8.640 53890 Z= 0.265 Chirality : 0.039 0.175 5842 Planarity : 0.004 0.055 6572 Dihedral : 13.745 160.557 6347 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.82 % Favored : 96.16 % Rotamer: Outliers : 2.43 % Allowed : 15.43 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.13), residues: 4586 helix: 2.46 (0.10), residues: 2969 sheet: 0.42 (1.09), residues: 24 loop : -0.44 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 58 TYR 0.032 0.001 TYR w 129 PHE 0.027 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.004 0.001 HIS p 26 Details of bonding type rmsd covalent geometry : bond 0.00260 (39900) covalent geometry : angle 0.53932 (53878) SS BOND : bond 0.00624 ( 6) SS BOND : angle 1.38548 ( 12) hydrogen bonds : bond 0.04152 ( 2286) hydrogen bonds : angle 3.82288 ( 6678) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 738 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 83 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8564 (ttpt) REVERT: W 98 MET cc_start: 0.8469 (mmp) cc_final: 0.7829 (mmp) REVERT: W 134 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8500 (mp) REVERT: X 124 ASP cc_start: 0.8730 (m-30) cc_final: 0.8457 (m-30) REVERT: Y 96 GLU cc_start: 0.8795 (pm20) cc_final: 0.8315 (pm20) REVERT: Z 23 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8599 (mmtm) REVERT: c 84 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8441 (tm-30) REVERT: e 77 ASP cc_start: 0.9033 (t0) cc_final: 0.8633 (t0) REVERT: e 146 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8734 (mttm) REVERT: e 148 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7619 (tm-30) REVERT: i 11 MET cc_start: 0.8688 (mmp) cc_final: 0.8375 (mmm) REVERT: i 14 MET cc_start: 0.8623 (mtt) cc_final: 0.8384 (mtt) REVERT: i 95 MET cc_start: 0.8851 (tpp) cc_final: 0.8608 (tpp) REVERT: i 261 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8709 (ttp) REVERT: i 319 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7485 (t70) REVERT: i 321 LYS cc_start: 0.7879 (ptmm) cc_final: 0.7502 (ptmm) REVERT: j 68 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: j 107 THR cc_start: 0.8820 (p) cc_final: 0.8342 (p) REVERT: j 108 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: k 91 GLN cc_start: 0.8546 (pm20) cc_final: 0.7994 (pm20) REVERT: l 504 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8764 (tt) REVERT: l 579 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7559 (t0) REVERT: m 1 MET cc_start: 0.4253 (tmm) cc_final: 0.3831 (tmm) REVERT: m 34 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8698 (mp) REVERT: o 25 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7473 (pt) REVERT: p 123 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8288 (mp0) REVERT: r 324 SER cc_start: 0.9438 (t) cc_final: 0.9181 (t) REVERT: r 453 MET cc_start: 0.8968 (mmt) cc_final: 0.8722 (mmt) REVERT: s 287 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7456 (t70) REVERT: u 90 ASP cc_start: 0.8921 (t0) cc_final: 0.8470 (t0) REVERT: v 38 GLU cc_start: 0.8668 (pm20) cc_final: 0.8467 (pm20) REVERT: v 89 TYR cc_start: 0.9218 (t80) cc_final: 0.8978 (t80) REVERT: v 101 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8239 (mm-30) REVERT: w 76 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8344 (mt-10) REVERT: w 120 ASP cc_start: 0.8003 (t0) cc_final: 0.7575 (t0) REVERT: w 227 MET cc_start: 0.9016 (mpp) cc_final: 0.8394 (mpp) REVERT: w 246 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8276 (mm) REVERT: w 303 GLU cc_start: 0.8009 (tp30) cc_final: 0.7625 (tp30) REVERT: w 312 VAL cc_start: 0.9249 (OUTLIER) cc_final: 0.9046 (m) outliers start: 99 outliers final: 67 residues processed: 796 average time/residue: 0.2281 time to fit residues: 299.7198 Evaluate side-chains 796 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 717 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain h residue 47 ILE Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 319 HIS Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain j residue 108 GLN Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 545 SER Chi-restraints excluded: chain l residue 579 ASN Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 34 ILE Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 50 GLU Chi-restraints excluded: chain p residue 81 ILE Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 125 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 214 LEU Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 287 HIS Chi-restraints excluded: chain s residue 288 LEU Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 94 LEU Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 246 LEU Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 393 optimal weight: 6.9990 chunk 220 optimal weight: 0.0970 chunk 40 optimal weight: 0.0030 chunk 56 optimal weight: 0.5980 chunk 360 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 219 optimal weight: 0.7980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 83 ASN i 322 GLN k 83 ASN l 205 ASN l 400 ASN l 541 ASN ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 235 ASN ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.099943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.080104 restraints weight = 61065.088| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.84 r_work: 0.2773 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 39907 Z= 0.107 Angle : 0.537 9.562 53890 Z= 0.264 Chirality : 0.039 0.176 5842 Planarity : 0.004 0.054 6572 Dihedral : 13.265 158.955 6347 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.58 % Favored : 96.40 % Rotamer: Outliers : 2.21 % Allowed : 15.93 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.13), residues: 4586 helix: 2.50 (0.10), residues: 2973 sheet: 0.50 (1.11), residues: 24 loop : -0.39 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG m 173 TYR 0.027 0.001 TYR w 129 PHE 0.029 0.001 PHE l 335 TRP 0.019 0.001 TRP u 86 HIS 0.003 0.001 HIS p 26 Details of bonding type rmsd covalent geometry : bond 0.00233 (39900) covalent geometry : angle 0.53680 (53878) SS BOND : bond 0.00263 ( 6) SS BOND : angle 1.67390 ( 12) hydrogen bonds : bond 0.03894 ( 2286) hydrogen bonds : angle 3.77065 ( 6678) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 746 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 83 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8580 (ttpt) REVERT: V 131 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8685 (mm-30) REVERT: W 98 MET cc_start: 0.8414 (mmp) cc_final: 0.7795 (mmp) REVERT: W 130 ASN cc_start: 0.8384 (m-40) cc_final: 0.7895 (t0) REVERT: W 134 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8573 (mp) REVERT: X 124 ASP cc_start: 0.8700 (m-30) cc_final: 0.8420 (m-30) REVERT: Y 96 GLU cc_start: 0.8751 (pm20) cc_final: 0.8265 (pm20) REVERT: Z 23 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8598 (mmtm) REVERT: c 84 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8427 (tm-30) REVERT: e 77 ASP cc_start: 0.9044 (t0) cc_final: 0.8685 (t0) REVERT: e 78 LYS cc_start: 0.9222 (ptmm) cc_final: 0.9013 (ptpp) REVERT: e 146 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8722 (mttm) REVERT: i 11 MET cc_start: 0.8726 (mmp) cc_final: 0.8278 (mtp) REVERT: i 14 MET cc_start: 0.8549 (mtt) cc_final: 0.8298 (mtt) REVERT: i 319 HIS cc_start: 0.7983 (OUTLIER) cc_final: 0.7468 (t70) REVERT: i 321 LYS cc_start: 0.7838 (ptmm) cc_final: 0.7513 (ptmm) REVERT: j 68 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: k 59 MET cc_start: 0.8258 (tmm) cc_final: 0.8026 (ttp) REVERT: k 83 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8034 (m110) REVERT: k 91 GLN cc_start: 0.8574 (pm20) cc_final: 0.8009 (pm20) REVERT: l 456 ARG cc_start: 0.8919 (mtm-85) cc_final: 0.8653 (mtm-85) REVERT: l 504 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8754 (tt) REVERT: l 579 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7576 (t0) REVERT: m 1 MET cc_start: 0.4366 (tmm) cc_final: 0.4015 (tmm) REVERT: m 34 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8564 (mp) REVERT: o 25 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7501 (pt) REVERT: p 123 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8285 (mp0) REVERT: r 256 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.7631 (p90) REVERT: r 324 SER cc_start: 0.9451 (t) cc_final: 0.9200 (t) REVERT: r 453 MET cc_start: 0.9018 (mmt) cc_final: 0.8786 (mmt) REVERT: s 234 MET cc_start: 0.8804 (mmt) cc_final: 0.8560 (mmt) REVERT: s 287 HIS cc_start: 0.8136 (OUTLIER) cc_final: 0.7365 (t70) REVERT: u 90 ASP cc_start: 0.8827 (t0) cc_final: 0.8359 (t0) REVERT: v 62 TYR cc_start: 0.8911 (m-80) cc_final: 0.8403 (m-80) REVERT: v 89 TYR cc_start: 0.9207 (t80) cc_final: 0.8981 (t80) REVERT: v 90 CYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8069 (t) REVERT: v 101 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8216 (mm-30) REVERT: w 76 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8356 (mt-10) REVERT: w 120 ASP cc_start: 0.8012 (t0) cc_final: 0.7576 (t0) REVERT: w 227 MET cc_start: 0.8979 (mpp) cc_final: 0.8546 (mpp) REVERT: w 246 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8267 (mm) REVERT: w 303 GLU cc_start: 0.8087 (tp30) cc_final: 0.7711 (tp30) REVERT: w 312 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.9017 (m) outliers start: 90 outliers final: 62 residues processed: 795 average time/residue: 0.2343 time to fit residues: 306.2416 Evaluate side-chains 792 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 717 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain h residue 47 ILE Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 319 HIS Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 83 ASN Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 545 SER Chi-restraints excluded: chain l residue 579 ASN Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 34 ILE Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 50 GLU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 214 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 287 HIS Chi-restraints excluded: chain s residue 288 LEU Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 246 LEU Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 231 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 64 optimal weight: 6.9990 chunk 263 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 chunk 224 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 0.0370 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 83 GLN c 94 HIS i 322 GLN j 108 GLN l 541 ASN r 399 ASN ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 235 ASN ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.080609 restraints weight = 60821.408| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.84 r_work: 0.2781 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 39907 Z= 0.108 Angle : 0.541 10.626 53890 Z= 0.264 Chirality : 0.039 0.175 5842 Planarity : 0.004 0.053 6572 Dihedral : 12.925 156.928 6347 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 2.16 % Allowed : 16.17 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.13), residues: 4586 helix: 2.50 (0.09), residues: 2976 sheet: 0.51 (1.10), residues: 24 loop : -0.37 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 173 TYR 0.023 0.001 TYR l 422 PHE 0.028 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.004 0.001 HIS p 26 Details of bonding type rmsd covalent geometry : bond 0.00239 (39900) covalent geometry : angle 0.54067 (53878) SS BOND : bond 0.00413 ( 6) SS BOND : angle 1.36622 ( 12) hydrogen bonds : bond 0.03829 ( 2286) hydrogen bonds : angle 3.75254 ( 6678) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 740 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 83 LYS cc_start: 0.8797 (ttpt) cc_final: 0.8588 (ttpt) REVERT: W 98 MET cc_start: 0.8396 (mmp) cc_final: 0.7784 (mmp) REVERT: W 130 ASN cc_start: 0.8388 (m-40) cc_final: 0.7864 (t0) REVERT: X 124 ASP cc_start: 0.8668 (m-30) cc_final: 0.8379 (m-30) REVERT: Y 96 GLU cc_start: 0.8753 (pm20) cc_final: 0.8271 (pm20) REVERT: Z 23 LYS cc_start: 0.8819 (mtpp) cc_final: 0.8571 (mmtm) REVERT: Z 35 LYS cc_start: 0.8862 (mtpt) cc_final: 0.8650 (mtpp) REVERT: c 84 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8487 (tm-30) REVERT: e 77 ASP cc_start: 0.9027 (t0) cc_final: 0.8676 (t0) REVERT: e 78 LYS cc_start: 0.9186 (ptmm) cc_final: 0.8984 (ptpp) REVERT: e 146 LYS cc_start: 0.9021 (mmmt) cc_final: 0.8720 (mttm) REVERT: e 148 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7605 (tm-30) REVERT: g 27 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8568 (mttp) REVERT: i 11 MET cc_start: 0.8735 (mmp) cc_final: 0.8288 (mtp) REVERT: i 14 MET cc_start: 0.8510 (mtt) cc_final: 0.8263 (mtt) REVERT: i 49 ASN cc_start: 0.7873 (p0) cc_final: 0.7661 (p0) REVERT: i 319 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7455 (t70) REVERT: i 321 LYS cc_start: 0.7772 (ptmm) cc_final: 0.7486 (ptmm) REVERT: j 68 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: k 59 MET cc_start: 0.8199 (tmm) cc_final: 0.7978 (ttp) REVERT: k 91 GLN cc_start: 0.8567 (pm20) cc_final: 0.7994 (pm20) REVERT: l 504 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8726 (tt) REVERT: l 579 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7540 (t0) REVERT: m 1 MET cc_start: 0.4383 (tmm) cc_final: 0.3656 (tpt) REVERT: m 34 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8539 (mp) REVERT: o 25 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7448 (pt) REVERT: p 123 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8274 (mp0) REVERT: r 256 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.7627 (p90) REVERT: r 324 SER cc_start: 0.9455 (t) cc_final: 0.9122 (t) REVERT: r 453 MET cc_start: 0.9010 (mmt) cc_final: 0.8777 (mmt) REVERT: s 270 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8192 (t80) REVERT: s 287 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.7433 (t70) REVERT: u 90 ASP cc_start: 0.8819 (t0) cc_final: 0.8357 (t0) REVERT: v 89 TYR cc_start: 0.9201 (t80) cc_final: 0.8973 (t80) REVERT: v 90 CYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8051 (t) REVERT: v 101 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8201 (mm-30) REVERT: w 76 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8355 (mt-10) REVERT: w 120 ASP cc_start: 0.8019 (t0) cc_final: 0.7580 (t0) REVERT: w 227 MET cc_start: 0.8986 (mpp) cc_final: 0.8559 (mpp) REVERT: w 246 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8290 (mm) REVERT: w 303 GLU cc_start: 0.8075 (tp30) cc_final: 0.7693 (tp30) REVERT: w 312 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.9004 (m) outliers start: 88 outliers final: 63 residues processed: 791 average time/residue: 0.2424 time to fit residues: 315.9379 Evaluate side-chains 803 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 727 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain g residue 27 LYS Chi-restraints excluded: chain h residue 47 ILE Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 319 HIS Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 545 SER Chi-restraints excluded: chain l residue 579 ASN Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 34 ILE Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 125 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 214 LEU Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 233 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 287 HIS Chi-restraints excluded: chain s residue 288 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 246 LEU Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 424 optimal weight: 0.9990 chunk 287 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 408 optimal weight: 2.9990 chunk 380 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 2 optimal weight: 0.0670 chunk 346 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 447 optimal weight: 0.0980 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 83 GLN i 322 GLN l 541 ASN p 51 HIS ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 235 ASN ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.080441 restraints weight = 61413.845| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.85 r_work: 0.2767 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 39907 Z= 0.112 Angle : 0.549 11.084 53890 Z= 0.268 Chirality : 0.039 0.175 5842 Planarity : 0.004 0.053 6572 Dihedral : 12.643 154.298 6347 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.62 % Favored : 96.36 % Rotamer: Outliers : 2.11 % Allowed : 16.42 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.13), residues: 4586 helix: 2.51 (0.09), residues: 2974 sheet: 0.42 (1.09), residues: 24 loop : -0.37 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 173 TYR 0.025 0.001 TYR n 26 PHE 0.029 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.004 0.001 HIS p 33 Details of bonding type rmsd covalent geometry : bond 0.00254 (39900) covalent geometry : angle 0.54848 (53878) SS BOND : bond 0.00312 ( 6) SS BOND : angle 1.43278 ( 12) hydrogen bonds : bond 0.03861 ( 2286) hydrogen bonds : angle 3.76379 ( 6678) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 737 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 64 LYS cc_start: 0.9231 (mmpt) cc_final: 0.8970 (mmtt) REVERT: V 83 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8563 (ttpt) REVERT: W 98 MET cc_start: 0.8425 (mmp) cc_final: 0.7848 (mmp) REVERT: W 130 ASN cc_start: 0.8332 (m-40) cc_final: 0.8083 (t0) REVERT: X 124 ASP cc_start: 0.8641 (m-30) cc_final: 0.8362 (m-30) REVERT: Y 96 GLU cc_start: 0.8756 (pm20) cc_final: 0.8278 (pm20) REVERT: Z 23 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8589 (mmtm) REVERT: Z 35 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8640 (mtpp) REVERT: c 84 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8491 (tm-30) REVERT: e 77 ASP cc_start: 0.9035 (t0) cc_final: 0.8689 (t0) REVERT: e 146 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8721 (mttm) REVERT: e 148 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7622 (tm-30) REVERT: g 27 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8579 (mttp) REVERT: i 11 MET cc_start: 0.8732 (mmp) cc_final: 0.8315 (mtt) REVERT: i 14 MET cc_start: 0.8546 (mtt) cc_final: 0.8299 (mtt) REVERT: i 49 ASN cc_start: 0.7891 (p0) cc_final: 0.7676 (p0) REVERT: i 282 MET cc_start: 0.8559 (mtt) cc_final: 0.8339 (mtm) REVERT: i 284 MET cc_start: 0.8468 (mmt) cc_final: 0.8155 (mmm) REVERT: i 319 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7481 (t70) REVERT: i 321 LYS cc_start: 0.7747 (ptmm) cc_final: 0.7513 (ptmm) REVERT: j 68 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: k 83 ASN cc_start: 0.8772 (m-40) cc_final: 0.8416 (m-40) REVERT: k 91 GLN cc_start: 0.8593 (pm20) cc_final: 0.8145 (pm20) REVERT: l 504 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8747 (tt) REVERT: l 579 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7523 (t0) REVERT: m 1 MET cc_start: 0.4491 (tmm) cc_final: 0.4017 (tpt) REVERT: m 34 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8533 (mp) REVERT: o 25 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7534 (pt) REVERT: p 123 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8260 (mp0) REVERT: r 256 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.7633 (p90) REVERT: r 453 MET cc_start: 0.9035 (mmt) cc_final: 0.8808 (mmt) REVERT: s 270 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8175 (t80) REVERT: s 274 ARG cc_start: 0.9159 (ttt180) cc_final: 0.8865 (tmm-80) REVERT: s 287 HIS cc_start: 0.8224 (OUTLIER) cc_final: 0.7397 (t70) REVERT: u 90 ASP cc_start: 0.8818 (t0) cc_final: 0.8354 (t0) REVERT: u 98 ARG cc_start: 0.8936 (ttp80) cc_final: 0.8733 (ptm160) REVERT: v 89 TYR cc_start: 0.9214 (t80) cc_final: 0.8976 (t80) REVERT: v 90 CYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8038 (t) REVERT: v 101 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8265 (mm-30) REVERT: w 76 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8346 (mt-10) REVERT: w 120 ASP cc_start: 0.8015 (t0) cc_final: 0.7575 (t0) REVERT: w 227 MET cc_start: 0.9024 (mpp) cc_final: 0.8544 (mpp) REVERT: w 246 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8266 (mm) REVERT: w 303 GLU cc_start: 0.8101 (tp30) cc_final: 0.7743 (tp30) REVERT: w 312 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.8978 (m) outliers start: 86 outliers final: 69 residues processed: 784 average time/residue: 0.2273 time to fit residues: 293.9149 Evaluate side-chains 813 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 731 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain g residue 27 LYS Chi-restraints excluded: chain h residue 47 ILE Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 319 HIS Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 545 SER Chi-restraints excluded: chain l residue 579 ASN Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 34 ILE Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 50 GLU Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 125 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 214 LEU Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 308 SER Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 233 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 287 HIS Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 246 LEU Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 185 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 226 optimal weight: 4.9990 chunk 363 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 312 optimal weight: 0.8980 chunk 281 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 391 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 83 GLN i 322 GLN l 541 ASN ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 235 ASN ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.099893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.080027 restraints weight = 61061.438| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.83 r_work: 0.2762 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39907 Z= 0.119 Angle : 0.558 12.030 53890 Z= 0.272 Chirality : 0.039 0.174 5842 Planarity : 0.004 0.053 6572 Dihedral : 12.491 152.767 6347 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 2.11 % Allowed : 16.52 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.13), residues: 4586 helix: 2.51 (0.09), residues: 2973 sheet: 0.40 (1.08), residues: 24 loop : -0.38 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 173 TYR 0.021 0.001 TYR l 422 PHE 0.029 0.001 PHE i 292 TRP 0.020 0.001 TRP u 86 HIS 0.004 0.001 HIS p 26 Details of bonding type rmsd covalent geometry : bond 0.00275 (39900) covalent geometry : angle 0.55806 (53878) SS BOND : bond 0.00221 ( 6) SS BOND : angle 1.48285 ( 12) hydrogen bonds : bond 0.03935 ( 2286) hydrogen bonds : angle 3.77479 ( 6678) Misc. bond : bond 0.00006 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 733 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 64 LYS cc_start: 0.9231 (mmpt) cc_final: 0.8968 (mmtt) REVERT: V 83 LYS cc_start: 0.8797 (ttpt) cc_final: 0.8569 (ttpt) REVERT: W 98 MET cc_start: 0.8453 (mmp) cc_final: 0.7872 (mmp) REVERT: W 130 ASN cc_start: 0.8326 (m-40) cc_final: 0.7911 (t0) REVERT: X 124 ASP cc_start: 0.8600 (m-30) cc_final: 0.8318 (m-30) REVERT: Y 96 GLU cc_start: 0.8751 (pm20) cc_final: 0.8271 (pm20) REVERT: Z 23 LYS cc_start: 0.8825 (mtpp) cc_final: 0.8589 (mmtm) REVERT: Z 35 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8632 (mtpp) REVERT: c 84 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8479 (tm-30) REVERT: e 77 ASP cc_start: 0.9022 (t0) cc_final: 0.8678 (t0) REVERT: e 146 LYS cc_start: 0.9103 (mmmt) cc_final: 0.8786 (mttm) REVERT: e 148 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7641 (tm-30) REVERT: g 27 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8588 (mttp) REVERT: i 11 MET cc_start: 0.8748 (mmp) cc_final: 0.8331 (mtt) REVERT: i 14 MET cc_start: 0.8555 (mtt) cc_final: 0.8303 (mtt) REVERT: i 282 MET cc_start: 0.8636 (mtt) cc_final: 0.8386 (mtm) REVERT: i 284 MET cc_start: 0.8430 (mmt) cc_final: 0.8143 (mmm) REVERT: i 319 HIS cc_start: 0.7872 (OUTLIER) cc_final: 0.7482 (t70) REVERT: i 321 LYS cc_start: 0.7744 (ptmm) cc_final: 0.7460 (ptmm) REVERT: j 68 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: k 83 ASN cc_start: 0.8838 (m-40) cc_final: 0.8495 (m-40) REVERT: l 504 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8722 (tt) REVERT: l 579 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7508 (t0) REVERT: m 1 MET cc_start: 0.4528 (tmm) cc_final: 0.3841 (tpt) REVERT: m 34 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8538 (mp) REVERT: o 25 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7489 (pt) REVERT: p 123 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8255 (mp0) REVERT: r 207 MET cc_start: 0.9235 (tpp) cc_final: 0.8998 (tpp) REVERT: r 256 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.7669 (p90) REVERT: r 453 MET cc_start: 0.9028 (mmt) cc_final: 0.8797 (mmt) REVERT: s 270 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8176 (t80) REVERT: s 274 ARG cc_start: 0.9155 (ttt180) cc_final: 0.8859 (tmm-80) REVERT: s 287 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.7409 (t-90) REVERT: u 90 ASP cc_start: 0.8826 (t0) cc_final: 0.8371 (t0) REVERT: v 89 TYR cc_start: 0.9223 (t80) cc_final: 0.8987 (t80) REVERT: v 90 CYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8066 (t) REVERT: v 101 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8261 (mm-30) REVERT: w 76 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8353 (mt-10) REVERT: w 120 ASP cc_start: 0.8017 (t0) cc_final: 0.7576 (t0) REVERT: w 227 MET cc_start: 0.9024 (mpp) cc_final: 0.8546 (mpp) REVERT: w 246 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8292 (mm) REVERT: w 303 GLU cc_start: 0.8129 (tp30) cc_final: 0.7780 (tp30) REVERT: w 312 VAL cc_start: 0.9218 (OUTLIER) cc_final: 0.8970 (m) outliers start: 86 outliers final: 66 residues processed: 782 average time/residue: 0.2397 time to fit residues: 308.2209 Evaluate side-chains 795 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 716 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 151 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain g residue 27 LYS Chi-restraints excluded: chain h residue 47 ILE Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 319 HIS Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 315 VAL Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 545 SER Chi-restraints excluded: chain l residue 579 ASN Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 20 PHE Chi-restraints excluded: chain m residue 34 ILE Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 125 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 200 ILE Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain r residue 308 SER Chi-restraints excluded: chain s residue 70 MET Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 174 MET Chi-restraints excluded: chain s residue 233 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain s residue 287 HIS Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 246 LEU Chi-restraints excluded: chain w residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 212 optimal weight: 1.9990 chunk 376 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 363 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 322 GLN l 541 ASN ** s 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 235 ASN ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.078763 restraints weight = 61515.485| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.84 r_work: 0.2750 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 39907 Z= 0.134 Angle : 0.573 12.849 53890 Z= 0.280 Chirality : 0.040 0.183 5842 Planarity : 0.004 0.053 6572 Dihedral : 12.418 153.037 6347 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.60 % Favored : 96.38 % Rotamer: Outliers : 1.97 % Allowed : 16.79 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.13), residues: 4586 helix: 2.48 (0.09), residues: 2971 sheet: 0.44 (1.10), residues: 24 loop : -0.41 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 173 TYR 0.021 0.001 TYR w 129 PHE 0.029 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.004 0.001 HIS p 26 Details of bonding type rmsd covalent geometry : bond 0.00318 (39900) covalent geometry : angle 0.57270 (53878) SS BOND : bond 0.00258 ( 6) SS BOND : angle 1.47770 ( 12) hydrogen bonds : bond 0.04183 ( 2286) hydrogen bonds : angle 3.80396 ( 6678) Misc. bond : bond 0.00025 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10643.03 seconds wall clock time: 182 minutes 55.43 seconds (10975.43 seconds total)