Starting phenix.real_space_refine on Sat Mar 7 06:47:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vye_32202/03_2026/7vye_32202.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vye_32202/03_2026/7vye_32202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vye_32202/03_2026/7vye_32202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vye_32202/03_2026/7vye_32202.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vye_32202/03_2026/7vye_32202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vye_32202/03_2026/7vye_32202.map" } resolution = 3.1 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= 0.005 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 31 5.49 5 S 285 5.16 5 C 25492 2.51 5 N 6204 2.21 5 O 6834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38846 Number of models: 1 Model: "" Number of chains: 43 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: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1015 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "W" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 945 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} 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: "X" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 699 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 600 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "b" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 879 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 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: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1012 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "w" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2583 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 134 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "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: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 149 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 245 Unusual residues: {'CDL': 2, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "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: 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: "s" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {' UQ': 1, 'PEE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 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=0.50 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.50 Time building chain proxies: 7.84, per 1000 atoms: 0.20 Number of scatterers: 38846 At special positions: 0 Unit cell: (190.133, 184.762, 141.794, 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 285 16.00 P 31 15.00 O 6834 8.00 N 6204 7.00 C 25492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=1.55 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 78 " - pdb=" SG CYS u 110 " distance=2.51 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=1.64 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " distance=2.02 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: 3.79 Conformation dependent library (CDL) restraints added in 1.7 seconds 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8814 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 7 sheets defined 70.8% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'Q' and resid 40 through 45 Processing helix chain 'Q' and resid 46 through 48 No H-bonds generated for 'chain 'Q' and resid 46 through 48' Processing helix chain 'Q' and resid 56 through 61 removed outlier: 4.323A pdb=" N HIS Q 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 1 through 4 Processing helix chain 'S' and resid 5 through 30 Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 42 through 56 removed outlier: 3.501A pdb=" N ASN S 46 " --> pdb=" O SER S 42 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 Processing helix chain 'U' and resid 3 through 14 Processing helix chain 'U' and resid 16 through 32 Processing helix chain 'U' and resid 33 through 35 No H-bonds generated for 'chain 'U' and resid 33 through 35' Processing helix chain 'U' and resid 38 through 48 Processing helix chain 'U' and resid 78 through 84 Processing helix chain 'V' and resid 3 through 12 removed outlier: 3.820A pdb=" N ILE V 12 " --> pdb=" O LYS V 8 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 44 Processing helix chain 'V' and resid 48 through 82 Processing helix chain 'V' and resid 86 through 106 removed outlier: 3.887A pdb=" N TYR V 90 " --> pdb=" O ASP V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 132 removed outlier: 3.606A pdb=" N GLY V 111 " --> pdb=" O SER V 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 99 Proline residue: W 73 - end of helix Processing helix chain 'W' and resid 120 through 125 removed outlier: 3.674A pdb=" N LEU W 124 " --> pdb=" O MET W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 129 through 143 removed outlier: 6.282A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.606A 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 Processing helix chain 'Y' and resid 77 through 82 Processing helix chain 'Y' and resid 88 through 92 Processing helix chain 'Z' and resid 18 through 22 removed outlier: 3.667A pdb=" N TRP Z 22 " --> pdb=" O TYR Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 28 through 38 Processing helix chain 'Z' and resid 45 through 49 removed outlier: 3.651A pdb=" N GLU Z 49 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 55 removed outlier: 4.405A pdb=" N GLY Z 55 " --> pdb=" O TRP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 56 through 59 removed outlier: 4.076A pdb=" N ASN Z 59 " --> pdb=" O GLY Z 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 56 through 59' 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 removed outlier: 3.547A pdb=" N THR a 78 " --> pdb=" O TYR a 74 " (cutoff:3.500A) Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 108 through 113 removed outlier: 4.026A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE a 113 " --> pdb=" O TRP a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 115 through 126 Processing helix chain 'a' and resid 128 through 164 removed outlier: 4.045A pdb=" N ASN a 132 " --> pdb=" O GLY a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 179 removed outlier: 3.730A pdb=" N LEU a 178 " --> pdb=" O ASP a 175 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE a 179 " --> pdb=" O LYS a 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 175 through 179' Processing helix chain 'b' and resid 5 through 25 Processing helix chain 'b' and resid 65 through 74 Processing helix chain 'b' and resid 75 through 89 Processing helix chain 'b' and resid 90 through 93 removed outlier: 3.529A pdb=" N LYS b 93 " --> pdb=" O VAL b 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 90 through 93' Processing helix chain 'c' and resid 33 through 37 Processing helix chain 'c' and resid 44 through 55 Processing helix chain 'c' and resid 125 through 150 Processing helix chain 'd' and resid 28 through 59 removed outlier: 4.240A pdb=" N TYR d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix removed outlier: 3.712A pdb=" N ASN d 59 " --> pdb=" O GLN d 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 77 Processing helix chain 'd' and resid 81 through 117 Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'd' and resid 125 through 144 Processing helix chain 'd' and resid 151 through 175 Processing helix chain 'e' and resid 65 through 70 removed outlier: 4.229A pdb=" N LYS e 69 " --> pdb=" O ASN e 65 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN e 70 " --> pdb=" O LEU e 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 65 through 70' Processing helix chain 'e' and resid 79 through 95 Processing helix chain 'e' and resid 97 through 108 Processing helix chain 'e' and resid 114 through 132 Processing helix chain 'e' and resid 143 through 147 Processing helix chain 'f' and resid 40 through 74 Processing helix chain 'g' and resid 3 through 7 removed outlier: 4.150A pdb=" N GLY g 6 " --> pdb=" O MET g 3 " (cutoff:3.500A) Processing helix chain 'g' and resid 17 through 23 Processing helix chain 'g' and resid 30 through 51 Processing helix chain 'g' and resid 59 through 99 Processing helix chain 'g' and resid 110 through 114 Processing helix chain 'h' and resid 5 through 11 Processing helix chain 'h' and resid 15 through 19 Processing helix chain 'h' and resid 25 through 29 Processing helix chain 'h' and resid 33 through 45 Processing helix chain 'h' and resid 48 through 56 Processing helix chain 'h' and resid 56 through 69 Processing helix chain 'h' and resid 69 through 90 Processing helix chain 'i' and resid 2 through 23 Processing helix chain 'i' and resid 25 through 45 removed outlier: 3.587A 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 93 through 107 Processing helix chain 'i' and resid 113 through 122 removed outlier: 4.386A 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 removed outlier: 3.508A pdb=" N LEU i 139 " --> pdb=" O LYS i 135 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 149 Processing helix chain 'i' and resid 150 through 170 removed outlier: 3.809A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) Processing helix chain 'i' and resid 174 through 192 Processing helix chain 'i' and resid 197 through 222 removed outlier: 3.657A 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: 3.539A pdb=" N THR i 241 " --> pdb=" O MET i 237 " (cutoff:3.500A) Processing helix chain 'i' and resid 259 through 273 removed outlier: 4.453A pdb=" N LYS i 263 " --> pdb=" O GLY i 259 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN i 273 " --> pdb=" O GLU i 269 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 301 removed outlier: 3.570A pdb=" N THR i 280 " --> pdb=" O ILE i 276 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 315 removed outlier: 4.061A 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 339 through 346 Processing helix chain 'j' and resid 2 through 24 Processing helix chain 'j' and resid 25 through 27 No H-bonds generated for 'chain 'j' and resid 25 through 27' Processing helix chain 'j' and resid 52 through 73 removed outlier: 3.974A pdb=" N PHE j 56 " --> pdb=" O SER j 52 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 79 removed outlier: 3.572A pdb=" N SER j 79 " --> pdb=" O LEU j 75 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 108 Processing helix chain 'k' and resid 2 through 22 removed outlier: 3.828A pdb=" N TYR k 22 " --> pdb=" O GLY k 18 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 51 removed outlier: 3.601A 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: 4.691A 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: 4.279A pdb=" N SER l 6 " --> pdb=" O ASN l 2 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 22 Processing helix chain 'l' and resid 23 through 24 No H-bonds generated for 'chain 'l' and resid 23 through 24' Processing helix chain 'l' and resid 25 through 29 Processing helix chain 'l' and resid 31 through 57 removed outlier: 4.294A 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: 3.796A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 134 removed outlier: 3.542A pdb=" N PHE l 117 " --> pdb=" O PHE l 113 " (cutoff:3.500A) Processing helix chain 'l' and resid 136 through 156 removed outlier: 3.559A pdb=" N GLY l 148 " --> pdb=" O TRP l 144 " (cutoff:3.500A) Processing helix chain 'l' and resid 161 through 194 removed outlier: 3.948A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 197 through 205 Processing helix chain 'l' and resid 209 through 225 removed outlier: 4.388A pdb=" N LEU l 213 " --> pdb=" O PRO l 209 " (cutoff:3.500A) Processing helix chain 'l' and resid 226 through 230 removed outlier: 3.695A pdb=" N HIS l 230 " --> pdb=" O PHE l 227 " (cutoff:3.500A) Processing helix chain 'l' and resid 231 through 236 Processing helix chain 'l' and resid 237 through 239 No H-bonds generated for 'chain 'l' and resid 237 through 239' Processing helix chain 'l' and resid 240 through 247 Processing helix chain 'l' and resid 254 through 263 Processing helix chain 'l' and resid 263 through 268 Processing helix chain 'l' and resid 270 through 293 removed outlier: 3.847A pdb=" N GLN l 274 " --> pdb=" O ASN l 270 " (cutoff:3.500A) Processing helix chain 'l' and resid 297 through 319 Processing helix chain 'l' and resid 321 through 350 removed outlier: 3.726A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 355 through 359 removed outlier: 3.562A pdb=" N MET l 359 " --> pdb=" O ILE l 356 " (cutoff:3.500A) Processing helix chain 'l' and resid 366 through 381 Processing helix chain 'l' and resid 388 through 401 removed outlier: 4.766A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 432 Processing helix chain 'l' and resid 447 through 472 removed outlier: 3.723A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 483 through 507 removed outlier: 5.247A pdb=" N ALA l 490 " --> pdb=" O MET l 486 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU l 491 " --> pdb=" O LYS l 487 " (cutoff:3.500A) removed outlier: 3.803A 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: 3.551A pdb=" N TYR l 539 " --> pdb=" O ARG l 535 " (cutoff:3.500A) Processing helix chain 'l' and resid 556 through 562 removed outlier: 3.859A pdb=" N LEU l 562 " --> pdb=" O LEU l 558 " (cutoff:3.500A) Processing helix chain 'l' and resid 562 through 579 Processing helix chain 'l' and resid 583 through 602 Processing helix chain 'm' and resid 4 through 22 Processing helix chain 'm' and resid 25 through 48 Processing helix chain 'm' and resid 49 through 75 removed outlier: 3.882A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.688A 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: 4.200A pdb=" N GLY m 174 " --> pdb=" O GLU m 170 " (cutoff:3.500A) Processing helix chain 'n' and resid 7 through 12 Processing helix chain 'n' and resid 15 through 33 Processing helix chain 'o' and resid 15 through 24 Proline residue: o 20 - end of helix Processing helix chain 'o' and resid 26 through 52 Processing helix chain 'o' and resid 62 through 74 Processing helix chain 'o' and resid 76 through 80 Processing helix chain 'o' and resid 83 through 119 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 11 through 31 Processing helix chain 'p' and resid 33 through 49 Processing helix chain 'p' and resid 56 through 63 removed outlier: 3.511A 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 94 through 98 removed outlier: 3.697A pdb=" N LYS p 98 " --> pdb=" O GLU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 100 through 107 Processing helix chain 'p' and resid 108 through 114 removed outlier: 3.845A pdb=" N MET p 114 " --> pdb=" O SER p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 115 through 144 removed outlier: 3.512A pdb=" N PHE p 119 " --> pdb=" O TYR p 115 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.934A 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: 4.197A 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: 3.550A 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: 4.168A pdb=" N LEU r 65 " --> pdb=" O LEU r 61 " (cutoff:3.500A) removed outlier: 3.867A 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: 3.654A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 114 through 125 Processing helix chain 'r' and resid 125 through 136 removed outlier: 3.951A pdb=" N THR r 129 " --> pdb=" O THR r 125 " (cutoff:3.500A) Processing helix chain 'r' and resid 141 through 172 removed outlier: 4.013A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.590A 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 205 removed outlier: 4.211A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 223 removed outlier: 4.060A 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: 4.184A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) Processing helix chain 'r' and resid 248 through 250 No H-bonds generated for 'chain 'r' and resid 248 through 250' Processing helix chain 'r' and resid 252 through 278 removed outlier: 4.222A pdb=" N TYR r 256 " --> pdb=" O PRO r 252 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR r 259 " --> pdb=" O ASN r 255 " (cutoff:3.500A) Proline residue: r 260 - end of helix removed outlier: 3.537A pdb=" N LEU r 264 " --> pdb=" O PRO r 260 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG r 278 " --> pdb=" O SER r 274 " (cutoff:3.500A) Processing helix chain 'r' and resid 281 through 304 removed outlier: 3.522A pdb=" N GLN r 304 " --> pdb=" O ALA r 300 " (cutoff:3.500A) Processing helix chain 'r' and resid 305 through 338 removed outlier: 3.653A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 347 through 352 removed outlier: 4.062A 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: 4.077A pdb=" N LEU r 395 " --> pdb=" O ILE r 391 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR r 414 " --> pdb=" O MET r 410 " (cutoff:3.500A) Processing helix chain 'r' and resid 430 through 448 Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 449 through 454 removed outlier: 6.445A pdb=" N LYS r 452 " --> pdb=" O LEU r 449 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.639A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 46 through 58 Processing helix chain 's' and resid 67 through 85 removed outlier: 3.580A pdb=" N PHE s 71 " --> pdb=" O SER s 67 " (cutoff:3.500A) Proline residue: s 75 - end of helix Processing helix chain 's' and resid 100 through 112 Processing helix chain 's' and resid 112 through 122 removed outlier: 4.434A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 125 through 155 removed outlier: 3.880A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 169 removed outlier: 3.748A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) Processing helix chain 's' and resid 173 through 178 removed outlier: 3.919A pdb=" N THR s 177 " --> pdb=" O TRP s 173 " (cutoff:3.500A) Processing helix chain 's' and resid 178 through 193 removed outlier: 3.513A 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: 4.371A pdb=" N TYR s 255 " --> pdb=" O THR s 251 " (cutoff:3.500A) Processing helix chain 's' and resid 281 through 312 removed outlier: 5.073A 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 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: 4.018A pdb=" N SER u 92 " --> pdb=" O CYS u 88 " (cutoff:3.500A) Processing helix chain 'u' and resid 100 through 115 removed outlier: 3.506A pdb=" N GLN u 104 " --> pdb=" O CYS u 100 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 11 Processing helix chain 'v' and resid 12 through 16 Processing helix chain 'v' and resid 18 through 22 removed outlier: 3.768A pdb=" N MET v 22 " --> pdb=" O PRO v 19 " (cutoff:3.500A) Processing helix chain 'v' and resid 26 through 30 removed outlier: 4.054A pdb=" N GLY v 30 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing helix chain 'v' and resid 42 through 49 Processing helix chain 'v' and resid 59 through 73 removed outlier: 3.603A 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 93 through 98 removed outlier: 3.651A pdb=" N THR w 98 " --> pdb=" O ASP w 95 " (cutoff:3.500A) Processing helix chain 'w' and resid 113 through 120 Processing helix chain 'w' and resid 126 through 154 removed outlier: 3.512A pdb=" N ARG w 130 " --> pdb=" O GLY w 126 " (cutoff:3.500A) Processing helix chain 'w' and resid 166 through 176 removed outlier: 4.141A pdb=" N LEU w 170 " --> pdb=" O ASP w 166 " (cutoff:3.500A) Processing helix chain 'w' and resid 180 through 196 Processing helix chain 'w' and resid 210 through 222 removed outlier: 3.701A 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 Processing helix chain 'w' and resid 244 through 251 removed outlier: 3.696A pdb=" N GLU w 248 " --> pdb=" O THR w 244 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 265 through 276 removed outlier: 3.909A pdb=" N VAL w 269 " --> pdb=" O ASP w 265 " (cutoff:3.500A) Processing helix chain 'w' and resid 282 through 286 Processing helix chain 'w' and resid 287 through 299 Processing helix chain 'w' and resid 300 through 305 removed outlier: 3.570A pdb=" N VAL w 304 " --> pdb=" O ASN w 300 " (cutoff:3.500A) Processing helix chain 'w' and resid 306 through 310 removed outlier: 3.957A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) removed outlier: 3.686A 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: 6.621A 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: 6.180A 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: 5.154A pdb=" N SER l 64 " --> pdb=" O PHE l 80 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE l 80 " --> pdb=" O SER l 64 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP l 66 " --> pdb=" O LEU l 78 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU l 76 " --> pdb=" O TRP l 68 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR l 70 " --> pdb=" O VAL l 74 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL l 74 " --> pdb=" O THR l 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 151 through 152 Processing sheet with id=AA5, first strand: chain 'i' and resid 307 through 308 Processing sheet with id=AA6, first strand: chain 'r' and resid 50 through 51 Processing sheet with id=AA7, first strand: chain 'w' and resid 84 through 86 removed outlier: 6.232A pdb=" N ARG w 84 " --> pdb=" O VAL w 158 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE w 60 " --> pdb=" O LEU w 159 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR w 61 " --> pdb=" O VAL w 205 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL w 207 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP w 63 " --> pdb=" O VAL w 207 " (cutoff:3.500A) 2297 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: 6.85 Time building geometry restraints manager: 4.93 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: 5885 1.31 - 1.43: 10769 1.43 - 1.56: 22533 1.56 - 1.69: 144 1.69 - 1.82: 516 Bond restraints: 39847 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=" C18 UQ s 403 " pdb=" C19 UQ s 403 " ideal model delta sigma weight residual 1.336 1.557 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" CA7 CDL i 401 " pdb=" OA8 CDL i 401 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CA7 CDL o 201 " pdb=" OA8 CDL o 201 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CA7 CDL a 201 " pdb=" OA8 CDL a 201 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 ... (remaining 39842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 53079 3.47 - 6.94: 624 6.94 - 10.41: 90 10.41 - 13.88: 14 13.88 - 17.35: 10 Bond angle restraints: 53817 Sorted by residual: angle pdb=" N GLY a 94 " pdb=" CA GLY a 94 " pdb=" C GLY a 94 " ideal model delta sigma weight residual 111.36 123.28 -11.92 1.17e+00 7.31e-01 1.04e+02 angle pdb=" N PHE a 92 " pdb=" CA PHE a 92 " pdb=" C PHE a 92 " ideal model delta sigma weight residual 111.36 120.80 -9.44 1.09e+00 8.42e-01 7.49e+01 angle pdb=" C TYR c 75 " pdb=" N PRO c 76 " pdb=" CA PRO c 76 " ideal model delta sigma weight residual 119.85 128.19 -8.34 1.01e+00 9.80e-01 6.82e+01 angle pdb=" C VAL s 87 " pdb=" N PRO s 88 " pdb=" CA PRO s 88 " ideal model delta sigma weight residual 118.85 127.65 -8.80 1.09e+00 8.42e-01 6.52e+01 angle pdb=" C11 CDL l 701 " pdb=" CA5 CDL l 701 " pdb=" OA6 CDL l 701 " ideal model delta sigma weight residual 111.33 121.99 -10.66 1.32e+00 5.72e-01 6.50e+01 ... (remaining 53812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 23355 35.92 - 71.83: 816 71.83 - 107.75: 56 107.75 - 143.66: 27 143.66 - 179.58: 9 Dihedral angle restraints: 24263 sinusoidal: 10625 harmonic: 13638 Sorted by residual: dihedral pdb=" CB CYS V 95 " pdb=" SG CYS V 95 " pdb=" SG CYS V 115 " pdb=" CB CYS V 115 " ideal model delta sinusoidal sigma weight residual -86.00 -26.46 -59.54 1 1.00e+01 1.00e-02 4.73e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 98.97 -158.97 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" CB CYS u 88 " pdb=" SG CYS u 88 " pdb=" SG CYS u 100 " pdb=" CB CYS u 100 " ideal model delta sinusoidal sigma weight residual -86.00 -140.49 54.49 1 1.00e+01 1.00e-02 4.02e+01 ... (remaining 24260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 5473 0.092 - 0.185: 330 0.185 - 0.277: 24 0.277 - 0.370: 8 0.370 - 0.462: 3 Chirality restraints: 5838 Sorted by residual: chirality pdb=" CA PHE a 92 " pdb=" N PHE a 92 " pdb=" C PHE a 92 " pdb=" CB PHE a 92 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CA TRP u 86 " pdb=" N TRP u 86 " pdb=" C TRP u 86 " pdb=" CB TRP u 86 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.13e+00 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 2.41 -0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 5835 not shown) Planarity restraints: 6574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 403 " -0.345 2.00e-02 2.50e+03 4.91e-01 3.01e+03 pdb=" C11 UQ s 403 " -0.225 2.00e-02 2.50e+03 pdb=" C7 UQ s 403 " -0.578 2.00e-02 2.50e+03 pdb=" C8 UQ s 403 " 0.716 2.00e-02 2.50e+03 pdb=" C9 UQ s 403 " 0.432 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 403 " -0.246 2.00e-02 2.50e+03 2.52e-01 7.96e+02 pdb=" C18 UQ s 403 " 0.202 2.00e-02 2.50e+03 pdb=" C19 UQ s 403 " 0.359 2.00e-02 2.50e+03 pdb=" C20 UQ s 403 " -0.020 2.00e-02 2.50e+03 pdb=" C21 UQ s 403 " -0.295 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 403 " 0.167 2.00e-02 2.50e+03 2.08e-01 5.38e+02 pdb=" C13 UQ s 403 " -0.100 2.00e-02 2.50e+03 pdb=" C14 UQ s 403 " -0.346 2.00e-02 2.50e+03 pdb=" C15 UQ s 403 " 0.045 2.00e-02 2.50e+03 pdb=" C16 UQ s 403 " 0.235 2.00e-02 2.50e+03 ... (remaining 6571 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 331 2.62 - 3.19: 34725 3.19 - 3.76: 60910 3.76 - 4.33: 86494 4.33 - 4.90: 143153 Nonbonded interactions: 325613 Sorted by model distance: nonbonded pdb=" OH TYR c 75 " pdb=" O ILE c 105 " model vdw 2.053 3.040 nonbonded pdb=" O27 8Q1 X 201 " pdb=" O33 8Q1 X 201 " model vdw 2.054 3.040 nonbonded pdb=" N PEE b 201 " pdb=" O2P PEE b 201 " model vdw 2.210 3.120 nonbonded pdb=" O LEU l 290 " pdb=" OG SER l 523 " model vdw 2.221 3.040 nonbonded pdb=" O MET r 14 " pdb=" OG SER r 18 " model vdw 2.223 3.040 ... (remaining 325608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 33.660 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.482 39855 Z= 0.468 Angle : 1.004 55.222 53831 Z= 0.529 Chirality : 0.049 0.462 5838 Planarity : 0.009 0.491 6574 Dihedral : 18.095 179.580 15428 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.30 % Favored : 95.57 % Rotamer: Outliers : 0.27 % Allowed : 0.76 % Favored : 98.97 % Cbeta Deviations : 0.05 % 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: 1.26 (0.13), residues: 4586 helix: 1.62 (0.10), residues: 2935 sheet: 0.45 (1.14), residues: 25 loop : -0.58 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG e 88 TYR 0.038 0.002 TYR s 277 PHE 0.033 0.002 PHE i 292 TRP 0.024 0.001 TRP w 353 HIS 0.006 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00730 (39847) covalent geometry : angle 0.93272 (53817) SS BOND : bond 0.29660 ( 7) SS BOND : angle 23.05782 ( 14) hydrogen bonds : bond 0.14241 ( 2297) hydrogen bonds : angle 5.62616 ( 6678) Misc. bond : bond 0.19641 ( 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 927 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 916 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 79 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6823 (mm-30) REVERT: V 35 ILE cc_start: 0.8309 (mt) cc_final: 0.8104 (mt) REVERT: V 124 LEU cc_start: 0.9244 (mt) cc_final: 0.9036 (mp) REVERT: X 146 ASP cc_start: 0.7348 (m-30) cc_final: 0.6860 (m-30) REVERT: X 150 ASP cc_start: 0.7843 (m-30) cc_final: 0.7574 (m-30) REVERT: Z 43 ASP cc_start: 0.7339 (p0) cc_final: 0.7082 (p0) REVERT: Z 72 LYS cc_start: 0.8040 (mptt) cc_final: 0.7832 (mptt) REVERT: Z 73 TRP cc_start: 0.6199 (m-10) cc_final: 0.5899 (t60) REVERT: b 24 LYS cc_start: 0.9081 (tptp) cc_final: 0.8782 (tptp) REVERT: b 93 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8250 (mtpt) REVERT: c 70 MET cc_start: 0.7783 (mmt) cc_final: 0.7538 (mmt) REVERT: c 110 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8650 (p0) REVERT: d 6 ASP cc_start: 0.8880 (t70) cc_final: 0.8609 (t0) REVERT: e 124 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7472 (mtt180) REVERT: f 63 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8416 (mtpp) REVERT: f 68 GLU cc_start: 0.8714 (tp30) cc_final: 0.8437 (tp30) REVERT: h 80 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7568 (mtmt) REVERT: h 97 HIS cc_start: 0.8064 (OUTLIER) cc_final: 0.6580 (m90) REVERT: j 7 LEU cc_start: 0.9465 (mt) cc_final: 0.9253 (mt) REVERT: j 90 MET cc_start: 0.9006 (mmp) cc_final: 0.8462 (mmp) REVERT: k 9 ILE cc_start: 0.9297 (mm) cc_final: 0.8961 (mm) REVERT: k 43 MET cc_start: 0.8604 (tpt) cc_final: 0.8111 (tpt) REVERT: l 20 MET cc_start: 0.8412 (mtt) cc_final: 0.8157 (mtt) REVERT: l 53 MET cc_start: 0.8987 (mtm) cc_final: 0.8715 (mtp) REVERT: l 62 ILE cc_start: 0.8943 (mm) cc_final: 0.8714 (pt) REVERT: l 268 GLU cc_start: 0.8629 (pt0) cc_final: 0.8420 (pt0) REVERT: l 397 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7775 (mt-10) REVERT: l 525 MET cc_start: 0.8136 (mmm) cc_final: 0.7812 (mmm) REVERT: l 550 SER cc_start: 0.9009 (t) cc_final: 0.8649 (m) REVERT: m 3 MET cc_start: 0.5123 (mpp) cc_final: 0.4155 (mmt) REVERT: o 5 LYS cc_start: 0.8140 (ttpp) cc_final: 0.7808 (tttm) REVERT: o 95 ILE cc_start: 0.9135 (mm) cc_final: 0.8859 (mt) REVERT: p 55 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7295 (mmtt) REVERT: p 65 ARG cc_start: 0.7774 (ttt-90) cc_final: 0.7492 (ttt-90) REVERT: p 159 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8348 (mttp) REVERT: r 180 HIS cc_start: 0.8625 (t-90) cc_final: 0.8377 (t-170) REVERT: s 70 MET cc_start: 0.7558 (mtt) cc_final: 0.7302 (mtt) REVERT: u 16 GLN cc_start: 0.7782 (tt0) cc_final: 0.7302 (tm-30) REVERT: v 22 MET cc_start: 0.8400 (mtt) cc_final: 0.7803 (ttm) REVERT: v 34 ARG cc_start: 0.6068 (ttt-90) cc_final: 0.2694 (mtp85) REVERT: v 54 GLN cc_start: 0.8667 (pt0) cc_final: 0.8385 (pm20) REVERT: w 221 LYS cc_start: 0.7542 (mtpt) cc_final: 0.6908 (mttp) REVERT: w 246 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8534 (mt) REVERT: w 303 GLU cc_start: 0.7328 (tt0) cc_final: 0.7123 (tp30) outliers start: 11 outliers final: 5 residues processed: 923 average time/residue: 0.2439 time to fit residues: 363.4287 Evaluate side-chains 743 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 735 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 95 GLU Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain w residue 246 LEU 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: 3.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN S 44 GLN V 129 GLN Y 83 HIS Z 21 GLN d 134 GLN d 149 HIS i 49 ASN i 319 HIS ** i 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 ASN l 25 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 580 GLN r 192 ASN s 194 ASN s 230 ASN s 235 ASN v 85 HIS w 127 ASN w 235 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.113792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.092830 restraints weight = 52446.886| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.25 r_work: 0.2805 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 39855 Z= 0.183 Angle : 0.631 9.612 53831 Z= 0.319 Chirality : 0.043 0.194 5838 Planarity : 0.005 0.075 6574 Dihedral : 17.013 167.665 6306 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.84 % Favored : 96.10 % Rotamer: Outliers : 1.13 % Allowed : 7.06 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.13), residues: 4586 helix: 1.86 (0.09), residues: 2977 sheet: 0.58 (1.13), residues: 25 loop : -0.47 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 60 TYR 0.024 0.002 TYR r 406 PHE 0.031 0.002 PHE i 292 TRP 0.023 0.001 TRP u 86 HIS 0.006 0.001 HIS Y 83 Details of bonding type rmsd covalent geometry : bond 0.00435 (39847) covalent geometry : angle 0.63070 (53817) SS BOND : bond 0.00889 ( 7) SS BOND : angle 2.05658 ( 14) hydrogen bonds : bond 0.05597 ( 2297) hydrogen bonds : angle 4.33453 ( 6678) Misc. bond : bond 0.00335 ( 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 797 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 751 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 79 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7351 (mm-30) REVERT: U 82 LYS cc_start: 0.9010 (mtmt) cc_final: 0.8800 (mtmt) REVERT: V 83 LYS cc_start: 0.7633 (mtmt) cc_final: 0.7364 (pttm) REVERT: W 85 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: X 150 ASP cc_start: 0.8284 (m-30) cc_final: 0.8011 (m-30) REVERT: Z 43 ASP cc_start: 0.7813 (p0) cc_final: 0.7605 (p0) REVERT: Z 72 LYS cc_start: 0.8344 (mptt) cc_final: 0.8083 (mptt) REVERT: Z 73 TRP cc_start: 0.6886 (m-10) cc_final: 0.6308 (t60) REVERT: a 185 THR cc_start: 0.8591 (p) cc_final: 0.8344 (p) REVERT: b 88 TYR cc_start: 0.9043 (m-80) cc_final: 0.8776 (m-80) REVERT: b 93 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8381 (mtpt) REVERT: d 62 TYR cc_start: 0.8732 (m-10) cc_final: 0.8512 (m-80) REVERT: e 124 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7854 (mtt180) REVERT: e 125 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.9015 (mt) REVERT: e 132 ASN cc_start: 0.8884 (m-40) cc_final: 0.8480 (m110) REVERT: f 63 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8722 (mtpp) REVERT: f 68 GLU cc_start: 0.9121 (tp30) cc_final: 0.8907 (tp30) REVERT: h 80 LYS cc_start: 0.8441 (mtpp) cc_final: 0.7696 (mtmt) REVERT: k 9 ILE cc_start: 0.9178 (mm) cc_final: 0.8839 (mm) REVERT: k 89 TYR cc_start: 0.8220 (m-80) cc_final: 0.7877 (m-80) REVERT: l 525 MET cc_start: 0.8790 (mmm) cc_final: 0.8496 (mmm) REVERT: l 550 SER cc_start: 0.9109 (t) cc_final: 0.8821 (m) REVERT: l 562 LEU cc_start: 0.8924 (tp) cc_final: 0.8698 (tp) REVERT: l 573 MET cc_start: 0.9034 (mmm) cc_final: 0.8749 (mmp) REVERT: m 3 MET cc_start: 0.4644 (mpp) cc_final: 0.3870 (mmt) REVERT: m 169 MET cc_start: 0.9179 (mmm) cc_final: 0.8894 (mtp) REVERT: o 5 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7874 (tttm) REVERT: o 95 ILE cc_start: 0.9125 (mm) cc_final: 0.8826 (mt) REVERT: p 43 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8705 (mp) REVERT: p 55 LYS cc_start: 0.7670 (mmtt) cc_final: 0.7422 (mmtt) REVERT: p 159 LYS cc_start: 0.8862 (ttmt) cc_final: 0.8371 (mttp) REVERT: r 10 MET cc_start: 0.9077 (mmp) cc_final: 0.8806 (mmp) REVERT: r 176 PHE cc_start: 0.8277 (t80) cc_final: 0.8031 (t80) REVERT: r 180 HIS cc_start: 0.8970 (t-90) cc_final: 0.8715 (t-170) REVERT: s 235 ASN cc_start: 0.8899 (m-40) cc_final: 0.8561 (m110) REVERT: u 16 GLN cc_start: 0.8328 (tt0) cc_final: 0.7891 (tm-30) REVERT: v 22 MET cc_start: 0.8457 (mtt) cc_final: 0.7901 (ttm) REVERT: v 34 ARG cc_start: 0.6385 (ttt-90) cc_final: 0.3158 (mtp85) REVERT: v 46 MET cc_start: 0.8369 (ttt) cc_final: 0.8053 (ttt) REVERT: v 54 GLN cc_start: 0.9131 (pt0) cc_final: 0.8838 (pm20) REVERT: w 221 LYS cc_start: 0.7848 (mtpt) cc_final: 0.7208 (mttp) REVERT: w 303 GLU cc_start: 0.8122 (tt0) cc_final: 0.7832 (tp30) outliers start: 46 outliers final: 31 residues processed: 778 average time/residue: 0.2347 time to fit residues: 298.6486 Evaluate side-chains 744 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 710 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain X residue 99 SER Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 576 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain r residue 350 THR Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain v residue 65 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 60 optimal weight: 4.9990 chunk 268 optimal weight: 0.9990 chunk 247 optimal weight: 6.9990 chunk 424 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 152 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 435 optimal weight: 7.9990 chunk 330 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 44 GLN S 68 ASN V 129 GLN d 134 GLN ** i 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 ASN l 580 GLN s 157 ASN s 194 ASN w 107 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.114072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.093169 restraints weight = 52361.851| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.29 r_work: 0.2788 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 39855 Z= 0.159 Angle : 0.585 8.939 53831 Z= 0.296 Chirality : 0.041 0.180 5838 Planarity : 0.005 0.067 6574 Dihedral : 15.964 166.899 6297 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.73 % Favored : 96.21 % Rotamer: Outliers : 1.45 % Allowed : 9.59 % Favored : 88.96 % 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: 1.80 (0.13), residues: 4586 helix: 2.05 (0.09), residues: 2961 sheet: 0.75 (1.11), residues: 25 loop : -0.43 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG h 81 TYR 0.026 0.001 TYR W 138 PHE 0.031 0.002 PHE i 292 TRP 0.025 0.001 TRP u 86 HIS 0.005 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00377 (39847) covalent geometry : angle 0.58329 (53817) SS BOND : bond 0.00787 ( 7) SS BOND : angle 2.65490 ( 14) hydrogen bonds : bond 0.05213 ( 2297) hydrogen bonds : angle 4.19721 ( 6678) Misc. bond : bond 0.00026 ( 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 811 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 752 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 79 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7441 (mm-30) REVERT: U 82 LYS cc_start: 0.9082 (mtmt) cc_final: 0.8812 (mtmt) REVERT: V 140 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8407 (ptmt) REVERT: W 85 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8378 (tt0) REVERT: X 150 ASP cc_start: 0.8281 (m-30) cc_final: 0.7998 (m-30) REVERT: Z 72 LYS cc_start: 0.8321 (mptt) cc_final: 0.8003 (mptt) REVERT: Z 73 TRP cc_start: 0.7060 (m-10) cc_final: 0.6399 (t60) REVERT: b 93 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8398 (mtpt) REVERT: c 173 ASP cc_start: 0.6902 (t70) cc_final: 0.6696 (t70) REVERT: e 83 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.7697 (t70) REVERT: e 124 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7818 (mtt180) REVERT: e 125 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9042 (mt) REVERT: e 132 ASN cc_start: 0.8872 (m-40) cc_final: 0.8510 (m110) REVERT: f 63 LYS cc_start: 0.9003 (ttmt) cc_final: 0.8714 (mtpp) REVERT: h 80 LYS cc_start: 0.8520 (mtpp) cc_final: 0.7910 (mtmt) REVERT: i 14 MET cc_start: 0.8906 (mtm) cc_final: 0.8704 (mtt) REVERT: k 9 ILE cc_start: 0.9151 (mm) cc_final: 0.8838 (mm) REVERT: k 89 TYR cc_start: 0.8256 (m-80) cc_final: 0.7931 (m-80) REVERT: l 69 MET cc_start: 0.9203 (ptt) cc_final: 0.8971 (ptt) REVERT: l 499 MET cc_start: 0.8691 (mtm) cc_final: 0.8449 (mtm) REVERT: l 544 MET cc_start: 0.8960 (mmt) cc_final: 0.8613 (mmp) REVERT: l 550 SER cc_start: 0.9121 (t) cc_final: 0.8778 (m) REVERT: l 573 MET cc_start: 0.9074 (mmm) cc_final: 0.8838 (mmm) REVERT: m 3 MET cc_start: 0.4769 (mpp) cc_final: 0.4079 (mmt) REVERT: m 169 MET cc_start: 0.9151 (mmm) cc_final: 0.8846 (mtp) REVERT: o 5 LYS cc_start: 0.8222 (ttpp) cc_final: 0.7869 (tttm) REVERT: o 95 ILE cc_start: 0.9087 (mm) cc_final: 0.8663 (mm) REVERT: p 43 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8701 (mp) REVERT: p 55 LYS cc_start: 0.7761 (mmtt) cc_final: 0.7399 (mmtt) REVERT: p 59 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8021 (ttmt) REVERT: r 10 MET cc_start: 0.9111 (mmp) cc_final: 0.8827 (mmp) REVERT: r 19 LYS cc_start: 0.8267 (mttm) cc_final: 0.7971 (mtpp) REVERT: v 22 MET cc_start: 0.8350 (mtt) cc_final: 0.7781 (ttm) REVERT: v 34 ARG cc_start: 0.6313 (ttt-90) cc_final: 0.3133 (mtp85) REVERT: v 54 GLN cc_start: 0.9125 (pt0) cc_final: 0.8765 (pm20) REVERT: w 160 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: w 221 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7245 (mttp) REVERT: w 303 GLU cc_start: 0.8210 (tt0) cc_final: 0.7899 (tp30) outliers start: 59 outliers final: 40 residues processed: 780 average time/residue: 0.2318 time to fit residues: 295.0997 Evaluate side-chains 752 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 707 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain Z residue 20 LYS Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 576 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 7 LYS Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain r residue 350 THR Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain w residue 160 GLU 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 182 optimal weight: 0.0040 chunk 353 optimal weight: 0.9990 chunk 349 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 392 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 288 optimal weight: 6.9990 chunk 441 optimal weight: 6.9990 chunk 305 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 44 GLN V 129 GLN X 101 ASN a 189 ASN d 134 GLN ** i 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 ASN l 479 ASN r 51 ASN r 251 ASN s 194 ASN w 142 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.114182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.093357 restraints weight = 51993.755| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.32 r_work: 0.2784 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 39855 Z= 0.149 Angle : 0.572 10.756 53831 Z= 0.289 Chirality : 0.041 0.178 5838 Planarity : 0.005 0.062 6574 Dihedral : 15.078 169.547 6296 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 1.89 % Allowed : 10.25 % Favored : 87.86 % 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: 1.92 (0.13), residues: 4586 helix: 2.12 (0.09), residues: 2974 sheet: 0.69 (1.10), residues: 25 loop : -0.35 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG h 81 TYR 0.023 0.001 TYR r 406 PHE 0.031 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.009 0.001 HIS Y 83 Details of bonding type rmsd covalent geometry : bond 0.00350 (39847) covalent geometry : angle 0.56925 (53817) SS BOND : bond 0.01043 ( 7) SS BOND : angle 3.68524 ( 14) hydrogen bonds : bond 0.04948 ( 2297) hydrogen bonds : angle 4.10581 ( 6678) Misc. bond : bond 0.00014 ( 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 808 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 731 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 79 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7326 (mm-30) REVERT: U 82 LYS cc_start: 0.9052 (mtmt) cc_final: 0.8775 (mtmt) REVERT: W 85 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: X 150 ASP cc_start: 0.8334 (m-30) cc_final: 0.8057 (m-30) REVERT: Z 72 LYS cc_start: 0.8345 (mptt) cc_final: 0.8025 (mptt) REVERT: Z 73 TRP cc_start: 0.7105 (m-10) cc_final: 0.6453 (t60) REVERT: b 91 THR cc_start: 0.9038 (m) cc_final: 0.8777 (m) REVERT: b 93 LYS cc_start: 0.8767 (ttmm) cc_final: 0.8315 (mtpt) REVERT: c 173 ASP cc_start: 0.6838 (t70) cc_final: 0.6607 (t70) REVERT: e 124 ARG cc_start: 0.8251 (mtm-85) cc_final: 0.7853 (mtt180) REVERT: e 132 ASN cc_start: 0.8863 (m-40) cc_final: 0.8520 (m110) REVERT: f 63 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8680 (mtpp) REVERT: h 13 ASP cc_start: 0.8767 (t70) cc_final: 0.8451 (t0) REVERT: h 80 LYS cc_start: 0.8513 (mtpp) cc_final: 0.7886 (mtmt) REVERT: j 97 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8518 (mp) REVERT: k 9 ILE cc_start: 0.9175 (mm) cc_final: 0.8876 (mm) REVERT: k 89 TYR cc_start: 0.8256 (m-80) cc_final: 0.7972 (m-80) REVERT: l 499 MET cc_start: 0.8753 (mtm) cc_final: 0.8506 (mtm) REVERT: l 525 MET cc_start: 0.8747 (mmm) cc_final: 0.8493 (mmm) REVERT: l 544 MET cc_start: 0.9023 (mmt) cc_final: 0.8599 (mmp) REVERT: l 550 SER cc_start: 0.9114 (t) cc_final: 0.8750 (m) REVERT: l 573 MET cc_start: 0.9105 (mmm) cc_final: 0.8883 (mmm) REVERT: m 1 MET cc_start: 0.3398 (OUTLIER) cc_final: 0.2028 (mmm) REVERT: m 3 MET cc_start: 0.4776 (mpp) cc_final: 0.4133 (mmt) REVERT: m 169 MET cc_start: 0.9202 (mmm) cc_final: 0.8880 (mtp) REVERT: o 5 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7867 (tttm) REVERT: o 95 ILE cc_start: 0.9085 (mm) cc_final: 0.8670 (mm) REVERT: p 3 PHE cc_start: 0.8842 (m-80) cc_final: 0.8638 (m-10) REVERT: p 43 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8724 (mp) REVERT: p 55 LYS cc_start: 0.7705 (mmtt) cc_final: 0.7423 (mmtt) REVERT: p 59 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8117 (ttmt) REVERT: r 10 MET cc_start: 0.9111 (mmp) cc_final: 0.8828 (mmp) REVERT: r 176 PHE cc_start: 0.8340 (t80) cc_final: 0.7998 (m-10) REVERT: r 448 THR cc_start: 0.9293 (t) cc_final: 0.8854 (m) REVERT: u 16 GLN cc_start: 0.8355 (tt0) cc_final: 0.7780 (tm-30) REVERT: u 103 GLN cc_start: 0.8908 (mp10) cc_final: 0.8645 (mp10) REVERT: v 22 MET cc_start: 0.8238 (mtt) cc_final: 0.7814 (ttm) REVERT: v 34 ARG cc_start: 0.6439 (ttt-90) cc_final: 0.3178 (mtp85) REVERT: v 54 GLN cc_start: 0.9130 (pt0) cc_final: 0.8802 (pm20) REVERT: v 88 ASP cc_start: 0.8741 (m-30) cc_final: 0.8474 (m-30) REVERT: w 160 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: w 221 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7014 (mttm) REVERT: w 303 GLU cc_start: 0.8227 (tt0) cc_final: 0.7929 (tp30) outliers start: 77 outliers final: 44 residues processed: 769 average time/residue: 0.2322 time to fit residues: 292.0455 Evaluate side-chains 760 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 711 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 20 LYS Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 576 MET Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 7 LYS Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain r residue 350 THR Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 194 ASN Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain v residue 65 GLN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 160 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 66 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 363 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 311 optimal weight: 2.9990 chunk 116 optimal weight: 0.4980 chunk 442 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 426 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 44 GLN V 129 GLN X 101 ASN d 134 GLN ** i 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 ASN l 479 ASN w 219 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.111604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.089951 restraints weight = 52185.084| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.34 r_work: 0.2754 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 39855 Z= 0.219 Angle : 0.629 8.868 53831 Z= 0.317 Chirality : 0.044 0.192 5838 Planarity : 0.005 0.057 6574 Dihedral : 14.838 169.430 6296 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.21 % Favored : 95.70 % Rotamer: Outliers : 2.06 % Allowed : 11.18 % Favored : 86.75 % 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: 1.73 (0.13), residues: 4586 helix: 1.98 (0.09), residues: 2969 sheet: 0.64 (1.12), residues: 25 loop : -0.43 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG h 81 TYR 0.022 0.002 TYR W 138 PHE 0.032 0.002 PHE i 292 TRP 0.019 0.002 TRP u 86 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00539 (39847) covalent geometry : angle 0.62738 (53817) SS BOND : bond 0.00845 ( 7) SS BOND : angle 3.17200 ( 14) hydrogen bonds : bond 0.05676 ( 2297) hydrogen bonds : angle 4.22363 ( 6678) Misc. bond : bond 0.00042 ( 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 790 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 706 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 79 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7472 (mm-30) REVERT: U 82 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8783 (mtmt) REVERT: W 85 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: X 101 ASN cc_start: 0.9221 (m110) cc_final: 0.8954 (m110) REVERT: X 150 ASP cc_start: 0.8359 (m-30) cc_final: 0.8062 (m-30) REVERT: Z 72 LYS cc_start: 0.8437 (mptt) cc_final: 0.8085 (mptt) REVERT: Z 73 TRP cc_start: 0.7062 (m-10) cc_final: 0.6381 (t60) REVERT: b 91 THR cc_start: 0.8969 (m) cc_final: 0.8676 (m) REVERT: b 93 LYS cc_start: 0.8796 (ttmm) cc_final: 0.8310 (mtpt) REVERT: c 173 ASP cc_start: 0.6983 (t70) cc_final: 0.6703 (t70) REVERT: e 83 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.7788 (t70) REVERT: e 132 ASN cc_start: 0.8874 (m-40) cc_final: 0.8536 (m110) REVERT: f 63 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8659 (mtpp) REVERT: h 13 ASP cc_start: 0.8768 (t0) cc_final: 0.8496 (t0) REVERT: h 97 HIS cc_start: 0.8326 (OUTLIER) cc_final: 0.6703 (m90) REVERT: k 89 TYR cc_start: 0.8275 (m-80) cc_final: 0.8025 (m-80) REVERT: l 69 MET cc_start: 0.9205 (ptt) cc_final: 0.8988 (ptt) REVERT: l 503 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7051 (tt0) REVERT: l 544 MET cc_start: 0.9076 (mmt) cc_final: 0.8626 (mmp) REVERT: l 550 SER cc_start: 0.9111 (t) cc_final: 0.8730 (m) REVERT: l 573 MET cc_start: 0.9151 (mmm) cc_final: 0.8921 (mmm) REVERT: m 3 MET cc_start: 0.4771 (mpp) cc_final: 0.4089 (mmt) REVERT: m 169 MET cc_start: 0.9211 (mmm) cc_final: 0.8876 (mtp) REVERT: o 95 ILE cc_start: 0.9112 (mm) cc_final: 0.8699 (mm) REVERT: p 43 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8690 (mp) REVERT: p 55 LYS cc_start: 0.7703 (mmtt) cc_final: 0.7379 (mmtt) REVERT: r 10 MET cc_start: 0.9236 (mmp) cc_final: 0.8945 (mmp) REVERT: r 176 PHE cc_start: 0.8360 (t80) cc_final: 0.7982 (m-10) REVERT: r 448 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8816 (m) REVERT: u 103 GLN cc_start: 0.9120 (mp10) cc_final: 0.8822 (mp10) REVERT: v 34 ARG cc_start: 0.6468 (ttt-90) cc_final: 0.3084 (mtp85) REVERT: v 54 GLN cc_start: 0.9188 (pt0) cc_final: 0.8811 (pm20) REVERT: w 160 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: w 221 LYS cc_start: 0.7878 (mtpt) cc_final: 0.7002 (mttm) REVERT: w 303 GLU cc_start: 0.8206 (tt0) cc_final: 0.7884 (tp30) outliers start: 84 outliers final: 54 residues processed: 755 average time/residue: 0.2316 time to fit residues: 286.8884 Evaluate side-chains 758 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 697 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 121 LYS Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 7 LYS Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 171 VAL Chi-restraints excluded: chain r residue 350 THR Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain v residue 65 GLN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 160 GLU 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 305 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 423 optimal weight: 0.3980 chunk 186 optimal weight: 0.1980 chunk 159 optimal weight: 2.9990 chunk 387 optimal weight: 0.8980 chunk 153 optimal weight: 0.3980 chunk 278 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 342 optimal weight: 0.6980 chunk 281 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 44 GLN V 129 GLN d 134 GLN ** i 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 ASN l 479 ASN u 64 ASN w 219 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.094660 restraints weight = 51764.058| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.28 r_work: 0.2831 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 39855 Z= 0.113 Angle : 0.535 8.423 53831 Z= 0.270 Chirality : 0.039 0.168 5838 Planarity : 0.004 0.067 6574 Dihedral : 14.095 172.134 6296 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.90 % Favored : 96.03 % Rotamer: Outliers : 1.72 % Allowed : 11.92 % Favored : 86.36 % 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: 2.05 (0.13), residues: 4586 helix: 2.26 (0.09), residues: 2966 sheet: 0.62 (1.09), residues: 25 loop : -0.36 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG h 81 TYR 0.025 0.001 TYR l 422 PHE 0.029 0.001 PHE i 292 TRP 0.022 0.001 TRP u 86 HIS 0.006 0.001 HIS Y 83 Details of bonding type rmsd covalent geometry : bond 0.00241 (39847) covalent geometry : angle 0.53352 (53817) SS BOND : bond 0.01143 ( 7) SS BOND : angle 2.69152 ( 14) hydrogen bonds : bond 0.04409 ( 2297) hydrogen bonds : angle 4.00562 ( 6678) Misc. bond : bond 0.00003 ( 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 804 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 734 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 28 LYS cc_start: 0.8778 (mmtp) cc_final: 0.8537 (ttmt) REVERT: U 79 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7404 (mm-30) REVERT: U 82 LYS cc_start: 0.8996 (mtmt) cc_final: 0.8730 (mtmt) REVERT: V 140 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8304 (ptmt) REVERT: X 150 ASP cc_start: 0.8312 (m-30) cc_final: 0.8007 (m-30) REVERT: Z 72 LYS cc_start: 0.8399 (mptt) cc_final: 0.8052 (mptt) REVERT: Z 73 TRP cc_start: 0.7039 (m-10) cc_final: 0.6339 (t60) REVERT: b 4 TYR cc_start: 0.8759 (m-80) cc_final: 0.8411 (m-80) REVERT: b 91 THR cc_start: 0.8883 (m) cc_final: 0.8571 (m) REVERT: b 93 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8122 (mtpt) REVERT: c 173 ASP cc_start: 0.6793 (t70) cc_final: 0.6537 (t70) REVERT: e 57 GLU cc_start: 0.8835 (tp30) cc_final: 0.8603 (tp30) REVERT: e 83 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7600 (t70) REVERT: e 125 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9062 (mt) REVERT: e 132 ASN cc_start: 0.8826 (m-40) cc_final: 0.8504 (m110) REVERT: f 63 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8628 (mtpp) REVERT: g 113 GLU cc_start: 0.8510 (pt0) cc_final: 0.8259 (pt0) REVERT: h 13 ASP cc_start: 0.8870 (t0) cc_final: 0.8472 (t0) REVERT: h 84 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8556 (m-30) REVERT: h 97 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.6635 (m90) REVERT: j 97 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8496 (mp) REVERT: k 9 ILE cc_start: 0.9003 (mm) cc_final: 0.8772 (mm) REVERT: k 89 TYR cc_start: 0.8203 (m-80) cc_final: 0.7943 (m-80) REVERT: l 108 MET cc_start: 0.9070 (mmt) cc_final: 0.8788 (mmt) REVERT: l 314 MET cc_start: 0.9213 (tpp) cc_final: 0.8990 (tpp) REVERT: l 525 MET cc_start: 0.8661 (mmm) cc_final: 0.8376 (mmm) REVERT: l 544 MET cc_start: 0.9068 (mmt) cc_final: 0.8716 (mmp) REVERT: l 550 SER cc_start: 0.9060 (t) cc_final: 0.8670 (m) REVERT: l 573 MET cc_start: 0.9149 (mmm) cc_final: 0.8909 (mmm) REVERT: m 1 MET cc_start: 0.3472 (OUTLIER) cc_final: 0.3163 (tmm) REVERT: m 3 MET cc_start: 0.4738 (mpp) cc_final: 0.3989 (mmt) REVERT: m 169 MET cc_start: 0.9109 (mmm) cc_final: 0.8728 (mtp) REVERT: o 95 ILE cc_start: 0.9014 (mm) cc_final: 0.8565 (mm) REVERT: p 55 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7490 (mmtt) REVERT: p 59 LYS cc_start: 0.8735 (tttp) cc_final: 0.8158 (ttmt) REVERT: r 10 MET cc_start: 0.9077 (mmp) cc_final: 0.8795 (mmp) REVERT: r 176 PHE cc_start: 0.8320 (t80) cc_final: 0.8028 (m-10) REVERT: r 448 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8919 (m) REVERT: s 302 MET cc_start: 0.9265 (mtm) cc_final: 0.9060 (mtt) REVERT: u 16 GLN cc_start: 0.8341 (tt0) cc_final: 0.7783 (tm-30) REVERT: v 34 ARG cc_start: 0.6503 (ttt-90) cc_final: 0.3147 (mtp85) REVERT: v 54 GLN cc_start: 0.9151 (pt0) cc_final: 0.8770 (pm20) REVERT: v 76 ASN cc_start: 0.8323 (t0) cc_final: 0.8104 (p0) REVERT: w 160 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: w 221 LYS cc_start: 0.7861 (mtpt) cc_final: 0.6995 (mttm) REVERT: w 303 GLU cc_start: 0.8161 (tt0) cc_final: 0.7841 (tp30) outliers start: 70 outliers final: 42 residues processed: 770 average time/residue: 0.2303 time to fit residues: 291.3054 Evaluate side-chains 753 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 703 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 20 LYS Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 121 LYS Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 138 GLU Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 576 MET Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 312 VAL Chi-restraints excluded: chain w residue 333 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 434 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 306 optimal weight: 8.9990 chunk 376 optimal weight: 0.7980 chunk 369 optimal weight: 7.9990 chunk 416 optimal weight: 0.0770 chunk 341 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 44 GLN V 129 GLN Z 59 ASN d 134 GLN ** i 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 ASN l 479 ASN s 194 ASN u 64 ASN w 219 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.114092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.093264 restraints weight = 51867.599| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.23 r_work: 0.2820 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 39855 Z= 0.148 Angle : 0.565 8.509 53831 Z= 0.284 Chirality : 0.041 0.241 5838 Planarity : 0.005 0.071 6574 Dihedral : 13.922 171.279 6296 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.84 % Rotamer: Outliers : 1.79 % Allowed : 12.29 % Favored : 85.91 % 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: 2.03 (0.13), residues: 4586 helix: 2.25 (0.09), residues: 2967 sheet: 0.55 (1.09), residues: 25 loop : -0.37 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG h 81 TYR 0.024 0.001 TYR W 138 PHE 0.031 0.001 PHE i 292 TRP 0.017 0.001 TRP u 86 HIS 0.005 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00351 (39847) covalent geometry : angle 0.56412 (53817) SS BOND : bond 0.00920 ( 7) SS BOND : angle 2.28783 ( 14) hydrogen bonds : bond 0.04795 ( 2297) hydrogen bonds : angle 4.05574 ( 6678) Misc. bond : bond 0.00029 ( 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 785 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 712 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 28 LYS cc_start: 0.8805 (mmtp) cc_final: 0.8560 (ttmt) REVERT: U 79 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7450 (mm-30) REVERT: U 82 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8753 (mtmt) REVERT: V 110 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7123 (tp) REVERT: W 85 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: X 150 ASP cc_start: 0.8341 (m-30) cc_final: 0.8056 (m-30) REVERT: Z 72 LYS cc_start: 0.8400 (mptt) cc_final: 0.8085 (mptt) REVERT: Z 73 TRP cc_start: 0.7080 (m-10) cc_final: 0.6401 (t60) REVERT: b 4 TYR cc_start: 0.8759 (m-80) cc_final: 0.8385 (m-80) REVERT: b 93 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8172 (mtpt) REVERT: c 173 ASP cc_start: 0.6876 (t70) cc_final: 0.6600 (t70) REVERT: e 83 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.7632 (t70) REVERT: e 132 ASN cc_start: 0.8826 (m-40) cc_final: 0.8512 (m110) REVERT: f 63 LYS cc_start: 0.8937 (ttmt) cc_final: 0.8635 (mtpp) REVERT: h 13 ASP cc_start: 0.8794 (t0) cc_final: 0.8417 (t0) REVERT: h 84 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8465 (m-30) REVERT: h 97 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.6626 (m90) REVERT: k 9 ILE cc_start: 0.9086 (mm) cc_final: 0.8798 (mm) REVERT: k 89 TYR cc_start: 0.8223 (m-80) cc_final: 0.7965 (m-80) REVERT: l 525 MET cc_start: 0.8737 (mmm) cc_final: 0.8482 (mmm) REVERT: l 544 MET cc_start: 0.9105 (mmt) cc_final: 0.8751 (mmp) REVERT: l 550 SER cc_start: 0.9068 (t) cc_final: 0.8688 (m) REVERT: l 573 MET cc_start: 0.9137 (mmm) cc_final: 0.8901 (mmm) REVERT: m 1 MET cc_start: 0.3451 (OUTLIER) cc_final: 0.2144 (mmm) REVERT: m 3 MET cc_start: 0.4735 (mpp) cc_final: 0.4148 (mmt) REVERT: m 169 MET cc_start: 0.9115 (mmm) cc_final: 0.8737 (mtp) REVERT: n 54 GLU cc_start: 0.7268 (mp0) cc_final: 0.6891 (mm-30) REVERT: o 95 ILE cc_start: 0.9053 (mm) cc_final: 0.8639 (mm) REVERT: p 55 LYS cc_start: 0.7917 (mmtt) cc_final: 0.7547 (mmtt) REVERT: p 59 LYS cc_start: 0.8811 (tttp) cc_final: 0.8243 (ttmt) REVERT: r 10 MET cc_start: 0.9085 (mmp) cc_final: 0.8796 (mmp) REVERT: r 176 PHE cc_start: 0.8311 (t80) cc_final: 0.8047 (m-10) REVERT: r 448 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8829 (m) REVERT: u 16 GLN cc_start: 0.8280 (tt0) cc_final: 0.7799 (tm-30) REVERT: v 34 ARG cc_start: 0.6495 (ttt-90) cc_final: 0.3061 (mtp85) REVERT: v 54 GLN cc_start: 0.9151 (pt0) cc_final: 0.8781 (pm20) REVERT: w 160 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: w 221 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7012 (mttm) REVERT: w 303 GLU cc_start: 0.8186 (tt0) cc_final: 0.7879 (tp30) outliers start: 73 outliers final: 50 residues processed: 747 average time/residue: 0.2358 time to fit residues: 288.7774 Evaluate side-chains 761 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 703 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Z residue 20 LYS Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 59 ASN Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain b residue 121 LYS Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 138 GLU Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 84 ASP Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 576 MET Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 7 LYS Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 194 ASN Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain v residue 65 GLN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 241 TYR 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 341 optimal weight: 4.9990 chunk 255 optimal weight: 0.9990 chunk 271 optimal weight: 0.0170 chunk 261 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 376 optimal weight: 1.9990 chunk 334 optimal weight: 5.9990 chunk 328 optimal weight: 0.8980 chunk 404 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 44 GLN V 129 GLN Z 59 ASN d 134 GLN ** i 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 ASN l 479 ASN u 64 ASN w 219 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.114907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.094178 restraints weight = 51717.624| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.23 r_work: 0.2835 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 39855 Z= 0.128 Angle : 0.552 8.373 53831 Z= 0.277 Chirality : 0.040 0.183 5838 Planarity : 0.005 0.069 6574 Dihedral : 13.715 171.705 6296 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.06 % Favored : 95.88 % Rotamer: Outliers : 1.84 % Allowed : 12.51 % Favored : 85.64 % 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: 2.10 (0.13), residues: 4586 helix: 2.32 (0.09), residues: 2955 sheet: 0.50 (1.07), residues: 25 loop : -0.36 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG h 81 TYR 0.023 0.001 TYR l 385 PHE 0.030 0.001 PHE i 292 TRP 0.019 0.001 TRP u 86 HIS 0.005 0.001 HIS Y 83 Details of bonding type rmsd covalent geometry : bond 0.00294 (39847) covalent geometry : angle 0.55007 (53817) SS BOND : bond 0.01078 ( 7) SS BOND : angle 2.54481 ( 14) hydrogen bonds : bond 0.04573 ( 2297) hydrogen bonds : angle 4.01366 ( 6678) Misc. bond : bond 0.00024 ( 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 793 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 718 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 28 LYS cc_start: 0.8796 (mmtp) cc_final: 0.8566 (ttmt) REVERT: U 79 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7441 (mm-30) REVERT: U 82 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8742 (mtmt) REVERT: V 110 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7112 (tp) REVERT: V 140 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8325 (ptmt) REVERT: W 85 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: X 150 ASP cc_start: 0.8325 (m-30) cc_final: 0.8069 (m-30) REVERT: Z 72 LYS cc_start: 0.8399 (mptt) cc_final: 0.8092 (mptt) REVERT: b 4 TYR cc_start: 0.8790 (m-80) cc_final: 0.8418 (m-80) REVERT: b 93 LYS cc_start: 0.8700 (ttmm) cc_final: 0.8172 (mtpt) REVERT: c 173 ASP cc_start: 0.6859 (t70) cc_final: 0.6578 (t70) REVERT: e 57 GLU cc_start: 0.8802 (tp30) cc_final: 0.8571 (tp30) REVERT: e 83 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7635 (t70) REVERT: e 125 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9083 (mt) REVERT: e 132 ASN cc_start: 0.8810 (m-40) cc_final: 0.8520 (m110) REVERT: f 63 LYS cc_start: 0.8932 (ttmt) cc_final: 0.8635 (mtpp) REVERT: h 13 ASP cc_start: 0.8781 (t0) cc_final: 0.8387 (t0) REVERT: h 84 ASP cc_start: 0.8764 (m-30) cc_final: 0.8473 (m-30) REVERT: h 97 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.6613 (m90) REVERT: j 97 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8542 (mp) REVERT: k 9 ILE cc_start: 0.9070 (mm) cc_final: 0.8771 (mm) REVERT: k 89 TYR cc_start: 0.8211 (m-80) cc_final: 0.7968 (m-80) REVERT: l 503 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: l 525 MET cc_start: 0.8681 (mmm) cc_final: 0.8445 (mmm) REVERT: l 544 MET cc_start: 0.9075 (mmt) cc_final: 0.8754 (mmp) REVERT: l 550 SER cc_start: 0.9056 (t) cc_final: 0.8662 (m) REVERT: l 573 MET cc_start: 0.9175 (mmm) cc_final: 0.8941 (mmm) REVERT: m 1 MET cc_start: 0.3392 (OUTLIER) cc_final: 0.2079 (mmm) REVERT: m 3 MET cc_start: 0.4777 (mpp) cc_final: 0.4246 (mmt) REVERT: m 169 MET cc_start: 0.9094 (mmm) cc_final: 0.8724 (mtp) REVERT: o 95 ILE cc_start: 0.9032 (mm) cc_final: 0.8602 (mm) REVERT: p 55 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7532 (mmtt) REVERT: p 59 LYS cc_start: 0.8830 (tttp) cc_final: 0.8272 (ttmt) REVERT: r 10 MET cc_start: 0.9082 (mmp) cc_final: 0.8804 (mmp) REVERT: r 176 PHE cc_start: 0.8310 (t80) cc_final: 0.8050 (m-10) REVERT: r 448 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8945 (m) REVERT: v 34 ARG cc_start: 0.6484 (ttt-90) cc_final: 0.3057 (mtp85) REVERT: v 54 GLN cc_start: 0.9085 (pt0) cc_final: 0.8751 (pm20) REVERT: w 160 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: w 221 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7032 (mttm) REVERT: w 303 GLU cc_start: 0.8188 (tt0) cc_final: 0.7886 (tp30) outliers start: 75 outliers final: 51 residues processed: 757 average time/residue: 0.2367 time to fit residues: 292.7167 Evaluate side-chains 767 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 706 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Z residue 20 LYS Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 121 LYS Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 138 GLU Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 576 MET Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 312 VAL Chi-restraints excluded: chain w residue 333 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 301 optimal weight: 0.9990 chunk 241 optimal weight: 3.9990 chunk 419 optimal weight: 5.9990 chunk 344 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 429 optimal weight: 0.7980 chunk 365 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 404 optimal weight: 6.9990 chunk 379 optimal weight: 3.9990 chunk 448 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 44 GLN V 129 GLN d 134 GLN ** i 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 ASN l 479 ASN s 194 ASN u 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.112280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.090200 restraints weight = 52197.545| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.39 r_work: 0.2752 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 39855 Z= 0.197 Angle : 0.615 9.398 53831 Z= 0.309 Chirality : 0.043 0.188 5838 Planarity : 0.005 0.070 6574 Dihedral : 13.903 170.717 6296 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 1.87 % Allowed : 12.56 % Favored : 85.57 % 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: 1.89 (0.13), residues: 4586 helix: 2.12 (0.09), residues: 2977 sheet: 0.49 (1.09), residues: 25 loop : -0.39 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG h 81 TYR 0.027 0.002 TYR l 385 PHE 0.032 0.002 PHE i 292 TRP 0.017 0.001 TRP u 86 HIS 0.006 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00480 (39847) covalent geometry : angle 0.61282 (53817) SS BOND : bond 0.01782 ( 7) SS BOND : angle 2.93469 ( 14) hydrogen bonds : bond 0.05365 ( 2297) hydrogen bonds : angle 4.14996 ( 6678) Misc. bond : bond 0.00052 ( 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 793 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 717 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 59 ASP cc_start: 0.7910 (t0) cc_final: 0.7614 (t0) REVERT: U 79 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7518 (mm-30) REVERT: U 82 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8749 (mtmt) REVERT: V 110 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7117 (tp) REVERT: W 85 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8364 (tt0) REVERT: X 150 ASP cc_start: 0.8380 (m-30) cc_final: 0.8077 (m-30) REVERT: Z 72 LYS cc_start: 0.8470 (mptt) cc_final: 0.8151 (mptt) REVERT: b 91 THR cc_start: 0.8852 (m) cc_final: 0.8554 (m) REVERT: b 93 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8270 (mtpt) REVERT: c 173 ASP cc_start: 0.7033 (t70) cc_final: 0.6693 (t70) REVERT: e 83 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.7733 (t70) REVERT: e 132 ASN cc_start: 0.8858 (m-40) cc_final: 0.8555 (m110) REVERT: f 63 LYS cc_start: 0.8941 (ttmt) cc_final: 0.8657 (mtpp) REVERT: h 13 ASP cc_start: 0.8750 (t0) cc_final: 0.8468 (t0) REVERT: h 97 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.6687 (m90) REVERT: k 9 ILE cc_start: 0.9105 (mm) cc_final: 0.8772 (mm) REVERT: l 503 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7042 (tt0) REVERT: l 544 MET cc_start: 0.9082 (mmt) cc_final: 0.8719 (mmp) REVERT: l 550 SER cc_start: 0.9109 (t) cc_final: 0.8703 (m) REVERT: l 573 MET cc_start: 0.9152 (mmm) cc_final: 0.8909 (mmm) REVERT: m 1 MET cc_start: 0.3511 (OUTLIER) cc_final: 0.2212 (mmm) REVERT: m 3 MET cc_start: 0.4638 (mpp) cc_final: 0.4127 (mmt) REVERT: m 169 MET cc_start: 0.9131 (mmm) cc_final: 0.8781 (mtp) REVERT: n 30 ARG cc_start: 0.8546 (mmm160) cc_final: 0.8205 (mtp180) REVERT: n 53 GLU cc_start: 0.7618 (tt0) cc_final: 0.7417 (tt0) REVERT: n 54 GLU cc_start: 0.7354 (mp0) cc_final: 0.6970 (mm-30) REVERT: o 95 ILE cc_start: 0.9058 (mm) cc_final: 0.8641 (mm) REVERT: p 55 LYS cc_start: 0.7930 (mmtt) cc_final: 0.7530 (mmtt) REVERT: p 59 LYS cc_start: 0.8763 (tttp) cc_final: 0.8251 (ttmt) REVERT: r 10 MET cc_start: 0.9142 (mmp) cc_final: 0.8855 (mmp) REVERT: r 19 LYS cc_start: 0.8288 (mttp) cc_final: 0.8045 (mttm) REVERT: r 176 PHE cc_start: 0.8358 (t80) cc_final: 0.8016 (m-10) REVERT: r 302 MET cc_start: 0.9238 (mmp) cc_final: 0.8987 (mmt) REVERT: r 448 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8849 (m) REVERT: u 16 GLN cc_start: 0.8375 (tt0) cc_final: 0.7809 (tm-30) REVERT: v 34 ARG cc_start: 0.6458 (ttt-90) cc_final: 0.2986 (mtp85) REVERT: v 54 GLN cc_start: 0.9124 (pt0) cc_final: 0.8753 (pm20) REVERT: w 160 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: w 221 LYS cc_start: 0.7952 (mtpt) cc_final: 0.7036 (mttm) REVERT: w 303 GLU cc_start: 0.8208 (tt0) cc_final: 0.7876 (tp30) outliers start: 76 outliers final: 57 residues processed: 754 average time/residue: 0.2373 time to fit residues: 292.3298 Evaluate side-chains 768 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 703 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 53 VAL Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 121 LYS Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 138 GLU Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 576 MET Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 7 LYS Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 194 ASN Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain v residue 65 GLN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 160 GLU 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 441 optimal weight: 2.9990 chunk 408 optimal weight: 2.9990 chunk 365 optimal weight: 0.0770 chunk 179 optimal weight: 0.6980 chunk 392 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 134 GLN ** i 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 ASN l 479 ASN s 157 ASN s 194 ASN u 64 ASN v 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.111251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.088987 restraints weight = 52137.548| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.31 r_work: 0.2765 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 39855 Z= 0.164 Angle : 0.689 59.200 53831 Z= 0.368 Chirality : 0.041 0.184 5838 Planarity : 0.005 0.102 6574 Dihedral : 13.892 170.682 6296 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 1.72 % Allowed : 12.71 % Favored : 85.57 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.13), residues: 4586 helix: 2.14 (0.09), residues: 2977 sheet: 0.49 (1.09), residues: 25 loop : -0.39 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG h 81 TYR 0.023 0.001 TYR l 385 PHE 0.032 0.002 PHE i 292 TRP 0.018 0.001 TRP u 86 HIS 0.006 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00359 (39847) covalent geometry : angle 0.68780 (53817) SS BOND : bond 0.01330 ( 7) SS BOND : angle 2.73724 ( 14) hydrogen bonds : bond 0.05202 ( 2297) hydrogen bonds : angle 4.14984 ( 6678) Misc. bond : bond 0.00020 ( 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 770 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 700 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 59 ASP cc_start: 0.7923 (t0) cc_final: 0.7645 (t0) REVERT: U 79 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7502 (mm-30) REVERT: U 82 LYS cc_start: 0.9022 (mtmt) cc_final: 0.8757 (mtmt) REVERT: V 110 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.7116 (tp) REVERT: W 85 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: X 150 ASP cc_start: 0.8365 (m-30) cc_final: 0.8066 (m-30) REVERT: Y 46 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8765 (pt0) REVERT: Z 72 LYS cc_start: 0.8464 (mptt) cc_final: 0.8145 (mptt) REVERT: b 91 THR cc_start: 0.8860 (m) cc_final: 0.8571 (m) REVERT: b 93 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8248 (mtpt) REVERT: c 173 ASP cc_start: 0.7009 (t70) cc_final: 0.6665 (t70) REVERT: e 83 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.7711 (t70) REVERT: e 132 ASN cc_start: 0.8856 (m-40) cc_final: 0.8558 (m110) REVERT: f 63 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8647 (mtpp) REVERT: h 13 ASP cc_start: 0.8743 (t0) cc_final: 0.8463 (t0) REVERT: h 97 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.6681 (m90) REVERT: k 9 ILE cc_start: 0.9106 (mm) cc_final: 0.8774 (mm) REVERT: l 503 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7004 (tt0) REVERT: l 544 MET cc_start: 0.9075 (mmt) cc_final: 0.8705 (mmp) REVERT: l 550 SER cc_start: 0.9102 (t) cc_final: 0.8693 (m) REVERT: l 573 MET cc_start: 0.9134 (mmm) cc_final: 0.8889 (mmm) REVERT: m 1 MET cc_start: 0.3490 (OUTLIER) cc_final: 0.2186 (mmm) REVERT: m 3 MET cc_start: 0.4632 (mpp) cc_final: 0.4129 (mmt) REVERT: m 169 MET cc_start: 0.9123 (mmm) cc_final: 0.8768 (mtp) REVERT: n 30 ARG cc_start: 0.8528 (mmm160) cc_final: 0.8186 (mtp180) REVERT: n 54 GLU cc_start: 0.7342 (mp0) cc_final: 0.6964 (mm-30) REVERT: o 95 ILE cc_start: 0.9050 (mm) cc_final: 0.8633 (mm) REVERT: p 55 LYS cc_start: 0.7987 (mmtt) cc_final: 0.7565 (mmtt) REVERT: p 59 LYS cc_start: 0.8754 (tttp) cc_final: 0.8244 (ttmt) REVERT: r 10 MET cc_start: 0.9131 (mmp) cc_final: 0.8844 (mmp) REVERT: r 19 LYS cc_start: 0.8279 (mttp) cc_final: 0.8028 (mttm) REVERT: r 176 PHE cc_start: 0.8344 (t80) cc_final: 0.8011 (m-10) REVERT: r 302 MET cc_start: 0.9227 (mmp) cc_final: 0.8976 (mmt) REVERT: r 448 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8842 (m) REVERT: s 194 ASN cc_start: 0.8286 (t0) cc_final: 0.8083 (t0) REVERT: u 16 GLN cc_start: 0.8374 (tt0) cc_final: 0.7809 (tm-30) REVERT: v 34 ARG cc_start: 0.6440 (ttt-90) cc_final: 0.2978 (mtp85) REVERT: v 54 GLN cc_start: 0.9117 (pt0) cc_final: 0.8742 (pm20) REVERT: w 160 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: w 221 LYS cc_start: 0.7947 (mtpt) cc_final: 0.7028 (mttm) REVERT: w 303 GLU cc_start: 0.8195 (tt0) cc_final: 0.7860 (tp30) outliers start: 70 outliers final: 56 residues processed: 740 average time/residue: 0.2291 time to fit residues: 277.8040 Evaluate side-chains 763 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 698 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 46 GLN Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 121 LYS Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain e residue 83 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 138 GLU Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 343 LEU Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 503 GLU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 576 MET Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 7 LYS Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 28 LEU Chi-restraints excluded: chain s residue 111 LEU Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain v residue 65 GLN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 241 TYR 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 386 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 262 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 341 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 398 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 134 GLN ** i 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 ASN l 479 ASN ** s 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 ASN v 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.111911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.089695 restraints weight = 52200.351| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.41 r_work: 0.2774 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 39855 Z= 0.164 Angle : 0.689 59.200 53831 Z= 0.368 Chirality : 0.041 0.184 5838 Planarity : 0.005 0.102 6574 Dihedral : 13.892 170.682 6296 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 1.62 % Allowed : 12.78 % Favored : 85.59 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.13), residues: 4586 helix: 2.14 (0.09), residues: 2977 sheet: 0.49 (1.09), residues: 25 loop : -0.39 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG h 81 TYR 0.023 0.001 TYR l 385 PHE 0.032 0.002 PHE i 292 TRP 0.018 0.001 TRP u 86 HIS 0.006 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00359 (39847) covalent geometry : angle 0.68780 (53817) SS BOND : bond 0.01330 ( 7) SS BOND : angle 2.73724 ( 14) hydrogen bonds : bond 0.05202 ( 2297) hydrogen bonds : angle 4.14984 ( 6678) Misc. bond : bond 0.00020 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11981.24 seconds wall clock time: 205 minutes 4.05 seconds (12304.05 seconds total)