Starting phenix.real_space_refine on Sun Aug 24 17:36:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8un1_42390/08_2025/8un1_42390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8un1_42390/08_2025/8un1_42390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8un1_42390/08_2025/8un1_42390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8un1_42390/08_2025/8un1_42390.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8un1_42390/08_2025/8un1_42390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8un1_42390/08_2025/8un1_42390.map" } resolution = 3.9 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= 0.002 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 14157 2.51 5 N 3632 2.21 5 O 4254 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22091 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "B" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1399 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "D" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "F" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "G" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "I" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "J" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "K" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "L" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "M" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "N" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "O" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "Q" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "R" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "S" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "T" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "U" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "V" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "W" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Time building chain proxies: 4.09, per 1000 atoms: 0.19 Number of scatterers: 22091 At special positions: 0 Unit cell: (140.18, 129, 135.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 4254 8.00 N 3632 7.00 C 14157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 918.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5526 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 35 sheets defined 41.6% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN A 40 " --> pdb=" O LYS A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 44 removed outlier: 3.521A pdb=" N GLY B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 81 Processing helix chain 'B' and resid 100 through 107 removed outlier: 4.473A pdb=" N PHE B 104 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 143 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU B 199 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN C 40 " --> pdb=" O LYS C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 90 Processing helix chain 'C' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.521A pdb=" N GLY D 33 " --> pdb=" O SER D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 81 Processing helix chain 'D' and resid 100 through 107 removed outlier: 4.472A pdb=" N PHE D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 143 Processing helix chain 'D' and resid 167 through 183 Processing helix chain 'D' and resid 184 through 186 No H-bonds generated for 'chain 'D' and resid 184 through 186' Processing helix chain 'D' and resid 196 through 200 removed outlier: 3.514A pdb=" N LEU D 199 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN E 40 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 90 Processing helix chain 'E' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 44 removed outlier: 3.522A pdb=" N GLY F 33 " --> pdb=" O SER F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 81 Processing helix chain 'F' and resid 100 through 107 removed outlier: 4.472A pdb=" N PHE F 104 " --> pdb=" O GLN F 100 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS F 106 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU F 107 " --> pdb=" O PRO F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 143 Processing helix chain 'F' and resid 167 through 183 Processing helix chain 'F' and resid 184 through 186 No H-bonds generated for 'chain 'F' and resid 184 through 186' Processing helix chain 'F' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU F 199 " --> pdb=" O VAL F 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 90 Processing helix chain 'G' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR G 117 " --> pdb=" O VAL G 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 40 removed outlier: 3.775A pdb=" N ASN I 40 " --> pdb=" O LYS I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 90 Processing helix chain 'I' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR I 117 " --> pdb=" O VAL I 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 44 removed outlier: 3.521A pdb=" N GLY J 33 " --> pdb=" O SER J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 81 Processing helix chain 'J' and resid 100 through 107 removed outlier: 4.472A pdb=" N PHE J 104 " --> pdb=" O GLN J 100 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS J 106 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU J 107 " --> pdb=" O PRO J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 143 Processing helix chain 'J' and resid 167 through 183 Processing helix chain 'J' and resid 184 through 186 No H-bonds generated for 'chain 'J' and resid 184 through 186' Processing helix chain 'J' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU J 199 " --> pdb=" O VAL J 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 40 removed outlier: 3.775A pdb=" N ASN K 40 " --> pdb=" O LYS K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 90 Processing helix chain 'K' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR K 117 " --> pdb=" O VAL K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 44 removed outlier: 3.522A pdb=" N GLY L 33 " --> pdb=" O SER L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 81 Processing helix chain 'L' and resid 100 through 107 removed outlier: 4.472A pdb=" N PHE L 104 " --> pdb=" O GLN L 100 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS L 106 " --> pdb=" O LEU L 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU L 107 " --> pdb=" O PRO L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 143 Processing helix chain 'L' and resid 167 through 183 Processing helix chain 'L' and resid 184 through 186 No H-bonds generated for 'chain 'L' and resid 184 through 186' Processing helix chain 'L' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU L 199 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN M 40 " --> pdb=" O LYS M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 90 Processing helix chain 'M' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR M 117 " --> pdb=" O VAL M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 removed outlier: 3.522A pdb=" N GLY N 33 " --> pdb=" O SER N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 81 Processing helix chain 'N' and resid 100 through 107 removed outlier: 4.472A pdb=" N PHE N 104 " --> pdb=" O GLN N 100 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS N 106 " --> pdb=" O LEU N 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU N 107 " --> pdb=" O PRO N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 143 Processing helix chain 'N' and resid 167 through 183 Processing helix chain 'N' and resid 184 through 186 No H-bonds generated for 'chain 'N' and resid 184 through 186' Processing helix chain 'N' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU N 199 " --> pdb=" O VAL N 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN O 40 " --> pdb=" O LYS O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 90 Processing helix chain 'O' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR O 117 " --> pdb=" O VAL O 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN Q 40 " --> pdb=" O LYS Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 90 Processing helix chain 'Q' and resid 106 through 117 removed outlier: 3.657A pdb=" N THR Q 117 " --> pdb=" O VAL Q 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 44 removed outlier: 3.521A pdb=" N GLY R 33 " --> pdb=" O SER R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 81 Processing helix chain 'R' and resid 100 through 107 removed outlier: 4.472A pdb=" N PHE R 104 " --> pdb=" O GLN R 100 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS R 106 " --> pdb=" O LEU R 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU R 107 " --> pdb=" O PRO R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 143 Processing helix chain 'R' and resid 167 through 183 Processing helix chain 'R' and resid 184 through 186 No H-bonds generated for 'chain 'R' and resid 184 through 186' Processing helix chain 'R' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU R 199 " --> pdb=" O VAL R 196 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN S 40 " --> pdb=" O LYS S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 90 Processing helix chain 'S' and resid 106 through 117 removed outlier: 3.657A pdb=" N THR S 117 " --> pdb=" O VAL S 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 44 removed outlier: 3.522A pdb=" N GLY T 33 " --> pdb=" O SER T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 81 Processing helix chain 'T' and resid 100 through 107 removed outlier: 4.472A pdb=" N PHE T 104 " --> pdb=" O GLN T 100 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS T 106 " --> pdb=" O LEU T 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU T 107 " --> pdb=" O PRO T 103 " (cutoff:3.500A) Processing helix chain 'T' and resid 128 through 143 Processing helix chain 'T' and resid 167 through 183 Processing helix chain 'T' and resid 184 through 186 No H-bonds generated for 'chain 'T' and resid 184 through 186' Processing helix chain 'T' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU T 199 " --> pdb=" O VAL T 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 40 removed outlier: 3.775A pdb=" N ASN U 40 " --> pdb=" O LYS U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 78 through 90 Processing helix chain 'U' and resid 106 through 117 removed outlier: 3.657A pdb=" N THR U 117 " --> pdb=" O VAL U 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 44 removed outlier: 3.521A pdb=" N GLY V 33 " --> pdb=" O SER V 29 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 81 Processing helix chain 'V' and resid 100 through 107 removed outlier: 4.473A pdb=" N PHE V 104 " --> pdb=" O GLN V 100 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS V 106 " --> pdb=" O LEU V 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU V 107 " --> pdb=" O PRO V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 128 through 143 Processing helix chain 'V' and resid 167 through 183 Processing helix chain 'V' and resid 184 through 186 No H-bonds generated for 'chain 'V' and resid 184 through 186' Processing helix chain 'V' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU V 199 " --> pdb=" O VAL V 196 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN W 40 " --> pdb=" O LYS W 36 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 90 Processing helix chain 'W' and resid 106 through 117 removed outlier: 3.657A pdb=" N THR W 117 " --> pdb=" O VAL W 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 24 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 18 through 24 current: chain 'I' and resid 67 through 74 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 67 through 74 current: chain 'Q' and resid 67 through 74 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 54 removed outlier: 5.289A pdb=" N LEU B 48 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 64 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 25 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 63 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 65 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 21 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 90 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 152 removed outlier: 5.699A pdb=" N LEU B 147 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE B 165 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER B 149 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 160 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 123 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP B 188 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 18 through 24 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 24 current: chain 'C' and resid 67 through 74 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 67 through 74 current: chain 'M' and resid 67 through 74 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 67 through 74 current: chain 'W' and resid 67 through 74 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 57 through 58 Processing sheet with id=AA7, first strand: chain 'D' and resid 47 through 54 removed outlier: 5.290A pdb=" N LEU D 48 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU D 64 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 25 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 63 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY D 65 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA D 21 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP D 90 " --> pdb=" O GLU D 26 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 146 through 152 removed outlier: 5.699A pdb=" N LEU D 147 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE D 165 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER D 149 " --> pdb=" O THR D 163 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA D 160 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL D 123 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP D 188 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 18 through 24 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 24 current: chain 'E' and resid 67 through 74 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 67 through 74 current: chain 'O' and resid 67 through 74 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 67 through 74 current: chain 'S' and resid 67 through 74 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 57 through 58 Processing sheet with id=AB2, first strand: chain 'F' and resid 47 through 54 removed outlier: 5.289A pdb=" N LEU F 48 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU F 64 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU F 25 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU F 63 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY F 65 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA F 21 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP F 90 " --> pdb=" O GLU F 26 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 146 through 152 removed outlier: 5.698A pdb=" N LEU F 147 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE F 165 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER F 149 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA F 160 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL F 123 " --> pdb=" O GLU F 190 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP F 188 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 104 through 105 removed outlier: 4.085A pdb=" N ASP K 104 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL G 99 " --> pdb=" O ASP K 104 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR G 74 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL G 67 " --> pdb=" O ALA G 51 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR G 73 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU G 45 " --> pdb=" O TYR G 73 " (cutoff:3.500A) removed outlier: 16.904A pdb=" N THR G 49 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 13.583A pdb=" N LEU K 52 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N ALA G 51 " --> pdb=" O PRO K 50 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR G 53 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE K 48 " --> pdb=" O THR G 53 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE G 55 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA K 46 " --> pdb=" O ILE G 55 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU K 45 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR K 73 " --> pdb=" O GLU K 45 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL K 67 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR K 74 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP U 104 " --> pdb=" O VAL K 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 57 through 58 Processing sheet with id=AB6, first strand: chain 'I' and resid 57 through 58 Processing sheet with id=AB7, first strand: chain 'J' and resid 47 through 54 removed outlier: 5.289A pdb=" N LEU J 48 " --> pdb=" O LEU J 64 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU J 64 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU J 25 " --> pdb=" O ILE J 61 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU J 63 " --> pdb=" O GLY J 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY J 65 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA J 21 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP J 90 " --> pdb=" O GLU J 26 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 146 through 152 removed outlier: 5.699A pdb=" N LEU J 147 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE J 165 " --> pdb=" O LEU J 147 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER J 149 " --> pdb=" O THR J 163 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA J 160 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL J 123 " --> pdb=" O GLU J 190 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP J 188 " --> pdb=" O GLU J 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 57 through 58 Processing sheet with id=AC1, first strand: chain 'L' and resid 47 through 54 removed outlier: 5.289A pdb=" N LEU L 48 " --> pdb=" O LEU L 64 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU L 64 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU L 25 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU L 63 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY L 65 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA L 21 " --> pdb=" O GLY L 65 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP L 90 " --> pdb=" O GLU L 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 146 through 152 removed outlier: 5.699A pdb=" N LEU L 147 " --> pdb=" O ILE L 165 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE L 165 " --> pdb=" O LEU L 147 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER L 149 " --> pdb=" O THR L 163 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA L 160 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL L 123 " --> pdb=" O GLU L 190 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP L 188 " --> pdb=" O GLU L 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 57 through 58 Processing sheet with id=AC4, first strand: chain 'N' and resid 47 through 54 removed outlier: 5.289A pdb=" N LEU N 48 " --> pdb=" O LEU N 64 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU N 64 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU N 25 " --> pdb=" O ILE N 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU N 63 " --> pdb=" O GLY N 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY N 65 " --> pdb=" O ALA N 21 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA N 21 " --> pdb=" O GLY N 65 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP N 90 " --> pdb=" O GLU N 26 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 146 through 152 removed outlier: 5.698A pdb=" N LEU N 147 " --> pdb=" O ILE N 165 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE N 165 " --> pdb=" O LEU N 147 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER N 149 " --> pdb=" O THR N 163 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA N 160 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL N 123 " --> pdb=" O GLU N 190 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP N 188 " --> pdb=" O GLU N 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 57 through 58 Processing sheet with id=AC7, first strand: chain 'Q' and resid 57 through 58 Processing sheet with id=AC8, first strand: chain 'R' and resid 47 through 54 removed outlier: 5.289A pdb=" N LEU R 48 " --> pdb=" O LEU R 64 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU R 64 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU R 25 " --> pdb=" O ILE R 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU R 63 " --> pdb=" O GLY R 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY R 65 " --> pdb=" O ALA R 21 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA R 21 " --> pdb=" O GLY R 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP R 90 " --> pdb=" O GLU R 26 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 146 through 152 removed outlier: 5.699A pdb=" N LEU R 147 " --> pdb=" O ILE R 165 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE R 165 " --> pdb=" O LEU R 147 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER R 149 " --> pdb=" O THR R 163 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA R 160 " --> pdb=" O VAL R 126 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL R 123 " --> pdb=" O GLU R 190 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP R 188 " --> pdb=" O GLU R 125 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 57 through 58 Processing sheet with id=AD2, first strand: chain 'T' and resid 47 through 54 removed outlier: 5.290A pdb=" N LEU T 48 " --> pdb=" O LEU T 64 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU T 64 " --> pdb=" O LEU T 48 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU T 25 " --> pdb=" O ILE T 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU T 63 " --> pdb=" O GLY T 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY T 65 " --> pdb=" O ALA T 21 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA T 21 " --> pdb=" O GLY T 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP T 90 " --> pdb=" O GLU T 26 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 146 through 152 removed outlier: 5.699A pdb=" N LEU T 147 " --> pdb=" O ILE T 165 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE T 165 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER T 149 " --> pdb=" O THR T 163 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA T 160 " --> pdb=" O VAL T 126 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL T 123 " --> pdb=" O GLU T 190 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP T 188 " --> pdb=" O GLU T 125 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 45 through 52 removed outlier: 4.437A pdb=" N GLU U 45 " --> pdb=" O TYR U 73 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR U 73 " --> pdb=" O GLU U 45 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL U 67 " --> pdb=" O ALA U 51 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR U 74 " --> pdb=" O ALA U 18 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 57 through 58 Processing sheet with id=AD6, first strand: chain 'V' and resid 47 through 54 removed outlier: 5.290A pdb=" N LEU V 48 " --> pdb=" O LEU V 64 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU V 64 " --> pdb=" O LEU V 48 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU V 25 " --> pdb=" O ILE V 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU V 63 " --> pdb=" O GLY V 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY V 65 " --> pdb=" O ALA V 21 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA V 21 " --> pdb=" O GLY V 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP V 90 " --> pdb=" O GLU V 26 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 146 through 152 removed outlier: 5.699A pdb=" N LEU V 147 " --> pdb=" O ILE V 165 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE V 165 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER V 149 " --> pdb=" O THR V 163 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA V 160 " --> pdb=" O VAL V 126 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL V 123 " --> pdb=" O GLU V 190 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP V 188 " --> pdb=" O GLU V 125 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 57 through 58 1096 hydrogen bonds defined for protein. 3153 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: 3.08 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.14: 12 1.14 - 1.31: 3909 1.31 - 1.48: 7860 1.48 - 1.65: 10564 1.65 - 1.82: 99 Bond restraints: 22444 Sorted by residual: bond pdb=" CG PRO U 25 " pdb=" CD PRO U 25 " ideal model delta sigma weight residual 1.503 0.974 0.529 3.40e-02 8.65e+02 2.42e+02 bond pdb=" CG PRO M 25 " pdb=" CD PRO M 25 " ideal model delta sigma weight residual 1.503 0.974 0.529 3.40e-02 8.65e+02 2.42e+02 bond pdb=" CG PRO A 25 " pdb=" CD PRO A 25 " ideal model delta sigma weight residual 1.503 0.974 0.529 3.40e-02 8.65e+02 2.42e+02 bond pdb=" CG PRO Q 25 " pdb=" CD PRO Q 25 " ideal model delta sigma weight residual 1.503 0.974 0.529 3.40e-02 8.65e+02 2.42e+02 bond pdb=" CG PRO I 25 " pdb=" CD PRO I 25 " ideal model delta sigma weight residual 1.503 0.974 0.529 3.40e-02 8.65e+02 2.42e+02 ... (remaining 22439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 30263 4.61 - 9.21: 255 9.21 - 13.82: 12 13.82 - 18.43: 24 18.43 - 23.03: 12 Bond angle restraints: 30566 Sorted by residual: angle pdb=" N PRO E 25 " pdb=" CD PRO E 25 " pdb=" CG PRO E 25 " ideal model delta sigma weight residual 103.20 80.17 23.03 1.50e+00 4.44e-01 2.36e+02 angle pdb=" N PRO S 25 " pdb=" CD PRO S 25 " pdb=" CG PRO S 25 " ideal model delta sigma weight residual 103.20 80.18 23.02 1.50e+00 4.44e-01 2.36e+02 angle pdb=" N PRO G 25 " pdb=" CD PRO G 25 " pdb=" CG PRO G 25 " ideal model delta sigma weight residual 103.20 80.18 23.02 1.50e+00 4.44e-01 2.36e+02 angle pdb=" N PRO O 25 " pdb=" CD PRO O 25 " pdb=" CG PRO O 25 " ideal model delta sigma weight residual 103.20 80.19 23.01 1.50e+00 4.44e-01 2.35e+02 angle pdb=" N PRO K 25 " pdb=" CD PRO K 25 " pdb=" CG PRO K 25 " ideal model delta sigma weight residual 103.20 80.19 23.01 1.50e+00 4.44e-01 2.35e+02 ... (remaining 30561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 11958 16.48 - 32.95: 1626 32.95 - 49.43: 414 49.43 - 65.91: 60 65.91 - 82.39: 33 Dihedral angle restraints: 14091 sinusoidal: 5607 harmonic: 8484 Sorted by residual: dihedral pdb=" CA LEU B 152 " pdb=" C LEU B 152 " pdb=" N ALA B 153 " pdb=" CA ALA B 153 " ideal model delta harmonic sigma weight residual 180.00 153.10 26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA LEU V 152 " pdb=" C LEU V 152 " pdb=" N ALA V 153 " pdb=" CA ALA V 153 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA LEU T 152 " pdb=" C LEU T 152 " pdb=" N ALA T 153 " pdb=" CA ALA T 153 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 14088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2765 0.053 - 0.105: 809 0.105 - 0.158: 132 0.158 - 0.211: 11 0.211 - 0.264: 36 Chirality restraints: 3753 Sorted by residual: chirality pdb=" CA PRO W 25 " pdb=" N PRO W 25 " pdb=" C PRO W 25 " pdb=" CB PRO W 25 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA PRO O 25 " pdb=" N PRO O 25 " pdb=" C PRO O 25 " pdb=" CB PRO O 25 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA PRO S 25 " pdb=" N PRO S 25 " pdb=" C PRO S 25 " pdb=" CB PRO S 25 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3750 not shown) Planarity restraints: 3918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR U 24 " -0.085 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO U 25 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO U 25 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO U 25 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR Q 24 " 0.085 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO Q 25 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO Q 25 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO Q 25 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR W 24 " 0.085 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO W 25 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO W 25 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO W 25 " 0.059 5.00e-02 4.00e+02 ... (remaining 3915 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 417 2.65 - 3.21: 21451 3.21 - 3.77: 34998 3.77 - 4.34: 44033 4.34 - 4.90: 70701 Nonbonded interactions: 171600 Sorted by model distance: nonbonded pdb=" NH1 ARG J 176 " pdb=" OXT THR Q 117 " model vdw 2.085 3.120 nonbonded pdb=" OG SER V 85 " pdb=" OD1 ASN V 87 " model vdw 2.140 3.040 nonbonded pdb=" OG SER T 85 " pdb=" OD1 ASN T 87 " model vdw 2.140 3.040 nonbonded pdb=" OG SER R 85 " pdb=" OD1 ASN R 87 " model vdw 2.140 3.040 nonbonded pdb=" OG SER N 85 " pdb=" OD1 ASN N 87 " model vdw 2.141 3.040 ... (remaining 171595 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) selection = (chain 'F' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) selection = (chain 'J' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) selection = (chain 'L' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) selection = (chain 'N' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) selection = (chain 'R' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) selection = (chain 'T' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) selection = (chain 'V' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 16.850 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 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 : 0.014 0.529 22444 Z= 0.465 Angle : 1.168 23.032 30566 Z= 0.672 Chirality : 0.054 0.264 3753 Planarity : 0.010 0.115 3918 Dihedral : 16.243 82.386 8565 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.47 % Allowed : 31.60 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.76 (0.16), residues: 2862 helix: 0.62 (0.15), residues: 1035 sheet: -1.03 (0.17), residues: 885 loop : -1.01 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 179 TYR 0.030 0.003 TYR C 109 PHE 0.021 0.004 PHE G 115 TRP 0.010 0.002 TRP C 112 HIS 0.004 0.001 HIS W 90 Details of bonding type rmsd covalent geometry : bond 0.01440 (22444) covalent geometry : angle 1.16825 (30566) hydrogen bonds : bond 0.19584 ( 1096) hydrogen bonds : angle 6.76464 ( 3153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 992 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7076 (tt0) cc_final: 0.6619 (tm-30) REVERT: A 62 ILE cc_start: 0.7990 (mm) cc_final: 0.7587 (mm) REVERT: A 63 LYS cc_start: 0.7203 (mmtt) cc_final: 0.6867 (mmpt) REVERT: B 62 MET cc_start: 0.8307 (tpp) cc_final: 0.8059 (mmp) REVERT: B 199 LEU cc_start: 0.9199 (pp) cc_final: 0.8907 (tp) REVERT: C 102 PRO cc_start: 0.5747 (Cg_endo) cc_final: 0.5457 (Cg_endo) REVERT: D 75 ILE cc_start: 0.8811 (mm) cc_final: 0.8293 (mm) REVERT: D 150 MET cc_start: 0.7573 (ttp) cc_final: 0.7323 (pmm) REVERT: D 151 ARG cc_start: 0.6230 (mtm-85) cc_final: 0.5913 (mtp-110) REVERT: E 35 LYS cc_start: 0.9045 (tptp) cc_final: 0.8648 (mttp) REVERT: E 36 LYS cc_start: 0.8279 (mmtm) cc_final: 0.7501 (tptp) REVERT: E 75 GLU cc_start: 0.8308 (pm20) cc_final: 0.7567 (pm20) REVERT: F 58 ARG cc_start: 0.7137 (mmp-170) cc_final: 0.6291 (mmm-85) REVERT: G 72 LEU cc_start: 0.8905 (mp) cc_final: 0.8651 (mp) REVERT: G 101 THR cc_start: 0.5163 (p) cc_final: 0.4617 (p) REVERT: I 42 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6486 (tp) REVERT: I 92 ASP cc_start: 0.7800 (m-30) cc_final: 0.6740 (t0) REVERT: K 63 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8706 (mmtp) REVERT: L 103 PRO cc_start: 0.8287 (Cg_exo) cc_final: 0.8025 (Cg_endo) REVERT: L 115 LYS cc_start: 0.9144 (ttpp) cc_final: 0.8829 (mmmt) REVERT: M 17 MET cc_start: 0.3645 (ptm) cc_final: 0.2734 (ptm) REVERT: M 87 LYS cc_start: 0.8852 (tptt) cc_final: 0.8518 (tttm) REVERT: M 97 ILE cc_start: 0.8333 (pt) cc_final: 0.8097 (pt) REVERT: N 26 GLU cc_start: 0.5822 (tm-30) cc_final: 0.5357 (tp30) REVERT: N 61 ILE cc_start: 0.8171 (tt) cc_final: 0.7811 (mp) REVERT: N 68 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8041 (tp30) REVERT: Q 19 ILE cc_start: 0.7772 (mm) cc_final: 0.7395 (mm) REVERT: R 58 ARG cc_start: 0.7682 (mmp-170) cc_final: 0.7220 (mmp-170) REVERT: T 24 ILE cc_start: 0.7981 (mp) cc_final: 0.7669 (mt) REVERT: T 148 THR cc_start: 0.8588 (p) cc_final: 0.8359 (p) REVERT: V 19 ARG cc_start: 0.7092 (mtm-85) cc_final: 0.6856 (mpp80) REVERT: V 96 GLU cc_start: 0.8199 (mm-30) cc_final: 0.6973 (pp20) REVERT: V 199 LEU cc_start: 0.7551 (pp) cc_final: 0.7106 (tp) REVERT: W 78 ASN cc_start: 0.8598 (t0) cc_final: 0.7924 (t0) outliers start: 11 outliers final: 3 residues processed: 996 average time/residue: 0.1625 time to fit residues: 236.7361 Evaluate side-chains 541 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 537 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain U residue 42 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN K 59 ASN O 59 ASN O 78 ASN R 100 GLN R 202 ASN S 59 ASN ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 ASN V 155 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.136158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.113160 restraints weight = 79466.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.116282 restraints weight = 52959.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.118572 restraints weight = 39109.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.120235 restraints weight = 30976.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.121481 restraints weight = 25792.150| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 22444 Z= 0.177 Angle : 0.861 11.611 30566 Z= 0.430 Chirality : 0.053 0.303 3753 Planarity : 0.007 0.073 3918 Dihedral : 5.907 53.231 3094 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.96 % Allowed : 25.85 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.46 (0.16), residues: 2862 helix: 0.75 (0.15), residues: 1032 sheet: -0.78 (0.18), residues: 861 loop : -0.80 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 69 TYR 0.032 0.003 TYR G 109 PHE 0.025 0.004 PHE N 104 TRP 0.015 0.002 TRP O 112 HIS 0.007 0.001 HIS F 155 Details of bonding type rmsd covalent geometry : bond 0.00432 (22444) covalent geometry : angle 0.86068 (30566) hydrogen bonds : bond 0.05243 ( 1096) hydrogen bonds : angle 5.15865 ( 3153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 594 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.5307 (mm) cc_final: 0.4774 (mm) REVERT: B 199 LEU cc_start: 0.9173 (pp) cc_final: 0.8861 (tp) REVERT: C 54 LYS cc_start: 0.8649 (ttpp) cc_final: 0.8195 (ttpp) REVERT: C 55 ILE cc_start: 0.9137 (mm) cc_final: 0.8698 (tp) REVERT: D 24 ILE cc_start: 0.8792 (mp) cc_final: 0.8414 (tt) REVERT: D 26 GLU cc_start: 0.6246 (mm-30) cc_final: 0.6040 (mm-30) REVERT: D 52 GLU cc_start: 0.5061 (OUTLIER) cc_final: 0.4640 (pm20) REVERT: D 60 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7950 (tp) REVERT: D 90 ASP cc_start: 0.7750 (t0) cc_final: 0.7456 (t0) REVERT: E 36 LYS cc_start: 0.8408 (mmtm) cc_final: 0.7608 (tptp) REVERT: E 76 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8115 (mm-30) REVERT: F 69 ASP cc_start: 0.6211 (OUTLIER) cc_final: 0.5847 (t70) REVERT: G 77 GLU cc_start: 0.8754 (mp0) cc_final: 0.7956 (pp20) REVERT: I 21 GLU cc_start: 0.7514 (tp30) cc_final: 0.7186 (tp30) REVERT: I 35 LYS cc_start: 0.8694 (pttp) cc_final: 0.8436 (ptpp) REVERT: I 42 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6784 (tp) REVERT: I 92 ASP cc_start: 0.7761 (m-30) cc_final: 0.6803 (t70) REVERT: J 24 ILE cc_start: 0.5503 (OUTLIER) cc_final: 0.4994 (mp) REVERT: J 168 LYS cc_start: 0.8264 (mppt) cc_final: 0.7994 (mmmt) REVERT: K 78 ASN cc_start: 0.7817 (m-40) cc_final: 0.7598 (m-40) REVERT: M 33 ILE cc_start: 0.8978 (mt) cc_final: 0.8759 (mm) REVERT: M 87 LYS cc_start: 0.9025 (tptt) cc_final: 0.8592 (tttm) REVERT: N 26 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6015 (tp30) REVERT: N 61 ILE cc_start: 0.8818 (tt) cc_final: 0.8516 (mp) REVERT: N 62 MET cc_start: 0.7831 (tpp) cc_final: 0.7474 (tpt) REVERT: N 68 GLU cc_start: 0.8886 (mm-30) cc_final: 0.7933 (tp30) REVERT: N 189 LEU cc_start: 0.8507 (tp) cc_final: 0.8237 (tp) REVERT: Q 21 GLU cc_start: 0.5660 (tp30) cc_final: 0.5094 (mp0) REVERT: Q 98 ILE cc_start: 0.8191 (mp) cc_final: 0.7933 (mp) REVERT: Q 115 PHE cc_start: 0.6346 (t80) cc_final: 0.5937 (t80) REVERT: R 58 ARG cc_start: 0.7713 (mmp-170) cc_final: 0.7293 (mmp80) REVERT: S 40 ASN cc_start: 0.8438 (p0) cc_final: 0.7973 (p0) REVERT: S 77 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: T 62 MET cc_start: 0.7486 (tpp) cc_final: 0.6907 (tpp) REVERT: T 176 ARG cc_start: 0.7440 (ptt90) cc_final: 0.6984 (ttm110) REVERT: U 35 LYS cc_start: 0.9103 (tptp) cc_final: 0.8660 (tptp) REVERT: V 19 ARG cc_start: 0.7432 (mtm-85) cc_final: 0.7035 (mpp80) REVERT: V 53 PRO cc_start: 0.5375 (Cg_endo) cc_final: 0.5058 (Cg_exo) REVERT: V 60 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6476 (tp) REVERT: V 74 MET cc_start: 0.9361 (mmm) cc_final: 0.9145 (mmm) REVERT: V 96 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7046 (pp20) REVERT: V 134 GLU cc_start: 0.8975 (tp30) cc_final: 0.8774 (mm-30) REVERT: V 199 LEU cc_start: 0.7774 (pp) cc_final: 0.7212 (tp) REVERT: W 42 LEU cc_start: 0.7238 (tp) cc_final: 0.6976 (tt) REVERT: W 45 GLU cc_start: 0.7587 (tp30) cc_final: 0.6358 (tm-30) REVERT: W 78 ASN cc_start: 0.8268 (t0) cc_final: 0.7538 (t0) outliers start: 140 outliers final: 62 residues processed: 688 average time/residue: 0.1482 time to fit residues: 155.9729 Evaluate side-chains 542 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 473 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 149 SER Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 65 GLU Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 73 TYR Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain T residue 48 LEU Chi-restraints excluded: chain T residue 97 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain V residue 48 LEU Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 92 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 38 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 180 optimal weight: 10.0000 chunk 232 optimal weight: 8.9990 chunk 199 optimal weight: 7.9990 chunk 248 optimal weight: 0.5980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 ASN I 59 ASN ** I 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 HIS M 59 ASN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN R 202 ASN ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.130998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.107525 restraints weight = 78690.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.110560 restraints weight = 52453.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.112844 restraints weight = 38872.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.114456 restraints weight = 30884.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.115734 restraints weight = 25863.163| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 22444 Z= 0.168 Angle : 0.788 10.441 30566 Z= 0.391 Chirality : 0.051 0.264 3753 Planarity : 0.006 0.062 3918 Dihedral : 5.669 59.813 3092 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 7.33 % Allowed : 26.66 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.31 (0.16), residues: 2862 helix: 0.89 (0.16), residues: 1032 sheet: -0.79 (0.16), residues: 918 loop : -0.60 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 151 TYR 0.024 0.002 TYR I 109 PHE 0.027 0.003 PHE E 115 TRP 0.020 0.002 TRP Q 112 HIS 0.027 0.002 HIS V 155 Details of bonding type rmsd covalent geometry : bond 0.00391 (22444) covalent geometry : angle 0.78807 (30566) hydrogen bonds : bond 0.04924 ( 1096) hydrogen bonds : angle 4.87338 ( 3153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 501 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.5341 (mm) cc_final: 0.4798 (mm) REVERT: B 69 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.6922 (t0) REVERT: B 199 LEU cc_start: 0.9231 (pp) cc_final: 0.8944 (tp) REVERT: C 54 LYS cc_start: 0.8727 (ttpp) cc_final: 0.8283 (ttpp) REVERT: C 55 ILE cc_start: 0.9215 (mm) cc_final: 0.8825 (tp) REVERT: D 24 ILE cc_start: 0.8960 (mp) cc_final: 0.8402 (tt) REVERT: D 52 GLU cc_start: 0.5027 (OUTLIER) cc_final: 0.4524 (pm20) REVERT: D 90 ASP cc_start: 0.7836 (t0) cc_final: 0.7556 (t0) REVERT: E 31 LYS cc_start: 0.9101 (tmmt) cc_final: 0.8821 (tmmt) REVERT: E 36 LYS cc_start: 0.8440 (mmtm) cc_final: 0.7879 (tptp) REVERT: E 76 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7946 (mm-30) REVERT: E 115 PHE cc_start: 0.7486 (t80) cc_final: 0.6220 (t80) REVERT: F 69 ASP cc_start: 0.6435 (OUTLIER) cc_final: 0.5995 (t70) REVERT: G 75 GLU cc_start: 0.8866 (tp30) cc_final: 0.7810 (pm20) REVERT: J 168 LYS cc_start: 0.8388 (mppt) cc_final: 0.8124 (mmmt) REVERT: K 77 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8288 (tp30) REVERT: K 78 ASN cc_start: 0.8031 (m-40) cc_final: 0.7825 (m-40) REVERT: L 63 LEU cc_start: 0.9057 (pt) cc_final: 0.8776 (pp) REVERT: L 69 ASP cc_start: 0.6769 (OUTLIER) cc_final: 0.6070 (t70) REVERT: N 26 GLU cc_start: 0.6763 (tm-30) cc_final: 0.6151 (tp30) REVERT: N 62 MET cc_start: 0.7715 (tpp) cc_final: 0.7441 (tpt) REVERT: N 93 LEU cc_start: 0.5376 (OUTLIER) cc_final: 0.5154 (pt) REVERT: N 151 ARG cc_start: 0.8318 (ppt170) cc_final: 0.8117 (ppt170) REVERT: R 58 ARG cc_start: 0.7653 (mmp-170) cc_final: 0.7315 (mmp80) REVERT: S 21 GLU cc_start: 0.8796 (tp30) cc_final: 0.8342 (tp30) REVERT: T 69 ASP cc_start: 0.6652 (OUTLIER) cc_final: 0.6193 (t0) REVERT: T 176 ARG cc_start: 0.7623 (ptt90) cc_final: 0.7358 (ttp80) REVERT: T 188 ASP cc_start: 0.8367 (m-30) cc_final: 0.8135 (m-30) REVERT: U 54 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8736 (mmmm) REVERT: U 104 ASP cc_start: 0.8704 (m-30) cc_final: 0.8501 (m-30) REVERT: V 53 PRO cc_start: 0.5572 (Cg_endo) cc_final: 0.5224 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6082 (mmp80) cc_final: 0.5191 (mtt180) REVERT: V 199 LEU cc_start: 0.7780 (pp) cc_final: 0.7245 (tp) REVERT: W 42 LEU cc_start: 0.7584 (tp) cc_final: 0.7021 (tt) REVERT: W 69 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7906 (ttm-80) REVERT: W 78 ASN cc_start: 0.8429 (t0) cc_final: 0.7667 (t0) REVERT: W 86 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8781 (pt) REVERT: W 109 TYR cc_start: 0.6912 (m-80) cc_final: 0.6695 (m-80) outliers start: 172 outliers final: 106 residues processed: 616 average time/residue: 0.1303 time to fit residues: 124.0658 Evaluate side-chains 551 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 438 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 149 SER Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 98 HIS Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 73 TYR Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 149 SER Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 202 ASN Chi-restraints excluded: chain W residue 31 LYS Chi-restraints excluded: chain W residue 35 LYS Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 86 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 136 optimal weight: 8.9990 chunk 128 optimal weight: 0.7980 chunk 251 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 230 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN F 155 HIS ** I 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN N 155 HIS O 78 ASN R 202 ASN S 78 ASN ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.130696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.107281 restraints weight = 81345.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.110307 restraints weight = 54612.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.112552 restraints weight = 40699.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.114167 restraints weight = 32479.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.115350 restraints weight = 27320.096| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22444 Z= 0.142 Angle : 0.748 11.094 30566 Z= 0.368 Chirality : 0.050 0.303 3753 Planarity : 0.006 0.055 3918 Dihedral : 5.391 56.003 3090 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 6.86 % Allowed : 27.47 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.10 (0.16), residues: 2862 helix: 1.06 (0.16), residues: 1032 sheet: -0.70 (0.16), residues: 936 loop : -0.44 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 179 TYR 0.021 0.002 TYR E 109 PHE 0.028 0.003 PHE E 115 TRP 0.024 0.002 TRP A 112 HIS 0.005 0.001 HIS W 90 Details of bonding type rmsd covalent geometry : bond 0.00327 (22444) covalent geometry : angle 0.74810 (30566) hydrogen bonds : bond 0.04338 ( 1096) hydrogen bonds : angle 4.64603 ( 3153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 476 time to evaluate : 0.813 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 32 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.5144 (mm) cc_final: 0.4476 (mm) REVERT: B 30 TYR cc_start: 0.8275 (t80) cc_final: 0.8037 (t80) REVERT: B 199 LEU cc_start: 0.9277 (pp) cc_final: 0.8971 (tp) REVERT: C 54 LYS cc_start: 0.8954 (ttpp) cc_final: 0.8521 (ttpp) REVERT: C 55 ILE cc_start: 0.9192 (mm) cc_final: 0.8692 (tp) REVERT: D 24 ILE cc_start: 0.8972 (mp) cc_final: 0.8387 (tt) REVERT: D 30 TYR cc_start: 0.8113 (t80) cc_final: 0.7906 (t80) REVERT: D 52 GLU cc_start: 0.4970 (OUTLIER) cc_final: 0.4697 (pm20) REVERT: D 90 ASP cc_start: 0.7764 (t0) cc_final: 0.7521 (t0) REVERT: E 36 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8045 (tptp) REVERT: E 115 PHE cc_start: 0.7613 (t80) cc_final: 0.6487 (t80) REVERT: F 62 MET cc_start: 0.8157 (tpp) cc_final: 0.7784 (tpp) REVERT: F 69 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6315 (t70) REVERT: F 90 ASP cc_start: 0.7515 (m-30) cc_final: 0.7200 (m-30) REVERT: G 36 LYS cc_start: 0.9326 (mmtm) cc_final: 0.8874 (tptp) REVERT: G 77 GLU cc_start: 0.8737 (mp0) cc_final: 0.8201 (pm20) REVERT: J 62 MET cc_start: 0.6163 (tpp) cc_final: 0.5540 (tpp) REVERT: L 63 LEU cc_start: 0.9083 (pt) cc_final: 0.8855 (pp) REVERT: L 69 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6046 (t70) REVERT: M 52 LEU cc_start: 0.6561 (mm) cc_final: 0.6254 (mp) REVERT: N 16 ASP cc_start: 0.6426 (p0) cc_final: 0.5049 (t0) REVERT: O 28 GLU cc_start: 0.8539 (pm20) cc_final: 0.7799 (pm20) REVERT: O 92 ASP cc_start: 0.7175 (m-30) cc_final: 0.6685 (t70) REVERT: Q 22 THR cc_start: 0.5521 (OUTLIER) cc_final: 0.5308 (p) REVERT: R 58 ARG cc_start: 0.7706 (mmp-170) cc_final: 0.7401 (mmp80) REVERT: R 140 LEU cc_start: 0.8097 (tp) cc_final: 0.7895 (tp) REVERT: S 17 MET cc_start: 0.2206 (ptm) cc_final: 0.1818 (mpp) REVERT: S 21 GLU cc_start: 0.8782 (tp30) cc_final: 0.8229 (tp30) REVERT: S 90 HIS cc_start: 0.7847 (t-90) cc_final: 0.7524 (t-90) REVERT: T 69 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.6343 (t0) REVERT: T 188 ASP cc_start: 0.8363 (m-30) cc_final: 0.8144 (m-30) REVERT: V 19 ARG cc_start: 0.7955 (mpp80) cc_final: 0.7078 (mpp80) REVERT: V 53 PRO cc_start: 0.5495 (Cg_endo) cc_final: 0.5179 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6202 (mmp80) cc_final: 0.5323 (ptp-170) REVERT: V 96 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7769 (pt0) REVERT: W 42 LEU cc_start: 0.7635 (tp) cc_final: 0.7198 (pp) REVERT: W 78 ASN cc_start: 0.8425 (t0) cc_final: 0.7663 (t0) REVERT: W 86 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8891 (pt) REVERT: W 109 TYR cc_start: 0.7135 (OUTLIER) cc_final: 0.6740 (m-80) outliers start: 161 outliers final: 96 residues processed: 572 average time/residue: 0.1480 time to fit residues: 129.7700 Evaluate side-chains 541 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 438 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 149 SER Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 98 HIS Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 73 TYR Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 202 ASN Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain W residue 109 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 140 optimal weight: 0.1980 chunk 117 optimal weight: 20.0000 chunk 262 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 217 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 260 optimal weight: 9.9990 chunk 266 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 HIS ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 155 HIS R 202 ASN ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.125110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.101883 restraints weight = 78918.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.104846 restraints weight = 52579.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.106997 restraints weight = 39022.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.108534 restraints weight = 31172.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.109663 restraints weight = 26284.505| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.6525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22444 Z= 0.184 Angle : 0.770 11.663 30566 Z= 0.384 Chirality : 0.051 0.293 3753 Planarity : 0.006 0.065 3918 Dihedral : 5.506 54.528 3090 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 7.20 % Allowed : 27.90 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.10 (0.16), residues: 2862 helix: 1.03 (0.16), residues: 1032 sheet: -0.53 (0.18), residues: 792 loop : -0.63 (0.21), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 179 TYR 0.021 0.002 TYR G 109 PHE 0.034 0.003 PHE E 115 TRP 0.024 0.002 TRP A 112 HIS 0.037 0.002 HIS V 155 Details of bonding type rmsd covalent geometry : bond 0.00428 (22444) covalent geometry : angle 0.76956 (30566) hydrogen bonds : bond 0.04728 ( 1096) hydrogen bonds : angle 4.75063 ( 3153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 452 time to evaluate : 0.734 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 32 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.5163 (mm) cc_final: 0.4696 (mm) REVERT: B 199 LEU cc_start: 0.9322 (pp) cc_final: 0.8966 (tp) REVERT: C 54 LYS cc_start: 0.9045 (ttpp) cc_final: 0.8694 (ttpp) REVERT: D 24 ILE cc_start: 0.8991 (mp) cc_final: 0.8442 (tt) REVERT: D 68 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8209 (tp30) REVERT: D 69 ASP cc_start: 0.7187 (m-30) cc_final: 0.6889 (m-30) REVERT: D 150 MET cc_start: 0.5731 (pmm) cc_final: 0.5384 (pmm) REVERT: E 115 PHE cc_start: 0.7181 (t80) cc_final: 0.6897 (t80) REVERT: F 69 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6808 (t0) REVERT: F 90 ASP cc_start: 0.7673 (m-30) cc_final: 0.7311 (m-30) REVERT: G 77 GLU cc_start: 0.8653 (mp0) cc_final: 0.8173 (pm20) REVERT: I 85 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6512 (m-80) REVERT: J 74 MET cc_start: 0.8494 (mmm) cc_final: 0.8161 (mmp) REVERT: L 63 LEU cc_start: 0.9112 (pt) cc_final: 0.8873 (pp) REVERT: M 52 LEU cc_start: 0.6711 (mm) cc_final: 0.6398 (mp) REVERT: M 87 LYS cc_start: 0.9150 (tppt) cc_final: 0.8593 (tttm) REVERT: O 28 GLU cc_start: 0.8548 (pm20) cc_final: 0.7958 (pm20) REVERT: O 92 ASP cc_start: 0.7371 (m-30) cc_final: 0.6863 (t70) REVERT: R 55 GLU cc_start: 0.4276 (OUTLIER) cc_final: 0.4068 (pm20) REVERT: R 58 ARG cc_start: 0.7490 (mmp-170) cc_final: 0.7223 (mmp80) REVERT: R 61 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9102 (pt) REVERT: R 142 LEU cc_start: 0.6370 (tp) cc_final: 0.6123 (tp) REVERT: S 17 MET cc_start: 0.2698 (ptm) cc_final: 0.2079 (mpp) REVERT: S 21 GLU cc_start: 0.8706 (tp30) cc_final: 0.8154 (tp30) REVERT: T 69 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6574 (t0) REVERT: U 104 ASP cc_start: 0.8746 (m-30) cc_final: 0.8520 (m-30) REVERT: U 115 PHE cc_start: 0.6243 (t80) cc_final: 0.6018 (t80) REVERT: V 19 ARG cc_start: 0.8101 (mpp80) cc_final: 0.7272 (mpp80) REVERT: V 53 PRO cc_start: 0.5626 (Cg_endo) cc_final: 0.5300 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6405 (mmp80) cc_final: 0.5582 (ptp-170) REVERT: V 96 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7909 (pt0) REVERT: V 112 GLU cc_start: 0.7654 (mp0) cc_final: 0.7357 (pp20) REVERT: W 78 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8240 (t0) outliers start: 169 outliers final: 109 residues processed: 557 average time/residue: 0.1474 time to fit residues: 125.4679 Evaluate side-chains 523 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 408 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 98 HIS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 202 ASN Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 78 ASN Chi-restraints excluded: chain W residue 86 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 139 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 194 optimal weight: 0.0000 chunk 36 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 247 optimal weight: 7.9990 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN V 155 HIS W 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.122765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.099807 restraints weight = 81927.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.102752 restraints weight = 53969.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.104894 restraints weight = 39779.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.106394 restraints weight = 31645.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.107579 restraints weight = 26614.767| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.7239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 22444 Z= 0.184 Angle : 0.760 11.490 30566 Z= 0.382 Chirality : 0.050 0.290 3753 Planarity : 0.006 0.059 3918 Dihedral : 5.636 55.592 3090 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 7.33 % Allowed : 28.15 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.10 (0.16), residues: 2862 helix: 1.12 (0.16), residues: 1023 sheet: -0.51 (0.18), residues: 747 loop : -0.75 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 179 TYR 0.021 0.002 TYR W 109 PHE 0.038 0.003 PHE E 115 TRP 0.018 0.002 TRP A 112 HIS 0.038 0.002 HIS V 155 Details of bonding type rmsd covalent geometry : bond 0.00424 (22444) covalent geometry : angle 0.75980 (30566) hydrogen bonds : bond 0.04584 ( 1096) hydrogen bonds : angle 4.73264 ( 3153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 448 time to evaluate : 0.771 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 32 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 THR cc_start: 0.3500 (OUTLIER) cc_final: 0.3285 (p) REVERT: A 94 ILE cc_start: 0.5129 (mm) cc_final: 0.4737 (mm) REVERT: A 116 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8076 (mm-30) REVERT: B 199 LEU cc_start: 0.9370 (pp) cc_final: 0.8955 (tp) REVERT: C 54 LYS cc_start: 0.8972 (ttpp) cc_final: 0.8509 (ttpp) REVERT: D 24 ILE cc_start: 0.9090 (mp) cc_final: 0.8394 (tt) REVERT: D 52 GLU cc_start: 0.4917 (OUTLIER) cc_final: 0.4605 (pm20) REVERT: F 90 ASP cc_start: 0.7750 (m-30) cc_final: 0.7435 (m-30) REVERT: F 159 ARG cc_start: 0.7987 (tpp80) cc_final: 0.7719 (tpp80) REVERT: G 77 GLU cc_start: 0.8763 (mp0) cc_final: 0.8332 (pm20) REVERT: I 85 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6678 (m-80) REVERT: J 19 ARG cc_start: 0.8732 (mpt-90) cc_final: 0.8296 (mpp80) REVERT: J 62 MET cc_start: 0.6061 (tpp) cc_final: 0.5560 (tpp) REVERT: J 74 MET cc_start: 0.8460 (mmm) cc_final: 0.8137 (mmp) REVERT: J 142 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7679 (mm) REVERT: K 17 MET cc_start: 0.3794 (mmm) cc_final: 0.1982 (pmm) REVERT: K 75 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7750 (pp20) REVERT: N 61 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8595 (mp) REVERT: N 74 MET cc_start: 0.9378 (mmt) cc_final: 0.9045 (mmt) REVERT: O 28 GLU cc_start: 0.8529 (pm20) cc_final: 0.8089 (pm20) REVERT: R 58 ARG cc_start: 0.7650 (mmp-170) cc_final: 0.7183 (mmp80) REVERT: S 17 MET cc_start: 0.2615 (ptm) cc_final: 0.2098 (mpp) REVERT: S 21 GLU cc_start: 0.8706 (tp30) cc_final: 0.8341 (tp30) REVERT: T 18 GLU cc_start: 0.7780 (mm-30) cc_final: 0.6951 (mt-10) REVERT: T 69 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6787 (t0) REVERT: U 54 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8696 (mmmt) REVERT: U 104 ASP cc_start: 0.8742 (m-30) cc_final: 0.8511 (m-30) REVERT: V 53 PRO cc_start: 0.5963 (Cg_endo) cc_final: 0.5640 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6645 (mmp80) cc_final: 0.5825 (ptp-170) REVERT: V 96 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8074 (pt0) REVERT: V 155 HIS cc_start: 0.4910 (OUTLIER) cc_final: 0.4472 (m90) REVERT: W 17 MET cc_start: 0.5270 (mpp) cc_final: 0.4158 (ttt) REVERT: W 40 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.8116 (m110) REVERT: W 78 ASN cc_start: 0.8424 (t0) cc_final: 0.7729 (t0) outliers start: 172 outliers final: 113 residues processed: 558 average time/residue: 0.1403 time to fit residues: 119.6930 Evaluate side-chains 530 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 408 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain V residue 26 GLU Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 151 ARG Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 202 ASN Chi-restraints excluded: chain W residue 40 ASN Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 55 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 281 optimal weight: 0.9990 chunk 267 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 204 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** F 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN L 100 GLN ** R 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.123341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.100246 restraints weight = 80464.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.103219 restraints weight = 53261.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.105380 restraints weight = 39351.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.106930 restraints weight = 31330.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.108106 restraints weight = 26289.000| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.7552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22444 Z= 0.148 Angle : 0.744 12.326 30566 Z= 0.366 Chirality : 0.049 0.316 3753 Planarity : 0.006 0.051 3918 Dihedral : 5.453 54.770 3090 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.35 % Allowed : 29.98 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: 0.04 (0.16), residues: 2862 helix: 1.27 (0.16), residues: 1032 sheet: -0.45 (0.19), residues: 747 loop : -0.73 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 179 TYR 0.022 0.002 TYR G 109 PHE 0.048 0.003 PHE E 115 TRP 0.019 0.002 TRP A 112 HIS 0.023 0.002 HIS V 155 Details of bonding type rmsd covalent geometry : bond 0.00349 (22444) covalent geometry : angle 0.74392 (30566) hydrogen bonds : bond 0.04201 ( 1096) hydrogen bonds : angle 4.57966 ( 3153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 430 time to evaluate : 0.896 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 32 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.5180 (mm) cc_final: 0.4809 (mm) REVERT: A 116 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8196 (mm-30) REVERT: B 199 LEU cc_start: 0.9384 (pp) cc_final: 0.8998 (tp) REVERT: C 54 LYS cc_start: 0.9002 (ttpp) cc_final: 0.8611 (ttpp) REVERT: D 24 ILE cc_start: 0.9025 (mp) cc_final: 0.8383 (tt) REVERT: D 62 MET cc_start: 0.7391 (ptp) cc_final: 0.7146 (ptt) REVERT: D 68 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8088 (tp30) REVERT: D 112 GLU cc_start: 0.3383 (pm20) cc_final: 0.2980 (pm20) REVERT: E 115 PHE cc_start: 0.7562 (t80) cc_final: 0.7290 (t80) REVERT: F 90 ASP cc_start: 0.7749 (m-30) cc_final: 0.7448 (m-30) REVERT: F 159 ARG cc_start: 0.7986 (tpp80) cc_final: 0.7735 (tpp80) REVERT: G 17 MET cc_start: 0.4584 (ttt) cc_final: 0.4024 (tpt) REVERT: G 77 GLU cc_start: 0.8769 (mp0) cc_final: 0.8399 (pm20) REVERT: I 85 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6486 (m-80) REVERT: J 19 ARG cc_start: 0.8756 (mpt-90) cc_final: 0.8321 (mpp80) REVERT: J 58 ARG cc_start: 0.6836 (mmp-170) cc_final: 0.6492 (mmp80) REVERT: J 74 MET cc_start: 0.8408 (mmm) cc_final: 0.8111 (mmp) REVERT: J 142 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7685 (mm) REVERT: J 170 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.5687 (t0) REVERT: K 17 MET cc_start: 0.3911 (mmm) cc_final: 0.1784 (pmm) REVERT: L 154 GLU cc_start: 0.5346 (pm20) cc_final: 0.4241 (pt0) REVERT: M 17 MET cc_start: 0.1146 (OUTLIER) cc_final: 0.0902 (ptm) REVERT: M 52 LEU cc_start: 0.6962 (mm) cc_final: 0.6737 (mt) REVERT: N 61 ILE cc_start: 0.8839 (tt) cc_final: 0.8613 (mp) REVERT: N 137 ASP cc_start: 0.8855 (t0) cc_final: 0.8617 (t0) REVERT: O 92 ASP cc_start: 0.7345 (m-30) cc_final: 0.6820 (t70) REVERT: Q 22 THR cc_start: 0.5604 (OUTLIER) cc_final: 0.5305 (p) REVERT: R 58 ARG cc_start: 0.7613 (mmp-170) cc_final: 0.7189 (mmp80) REVERT: R 69 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7676 (t70) REVERT: S 17 MET cc_start: 0.3139 (ptm) cc_final: 0.2773 (mpp) REVERT: T 18 GLU cc_start: 0.7725 (mm-30) cc_final: 0.6987 (mt-10) REVERT: T 69 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6786 (t0) REVERT: T 96 GLU cc_start: 0.8742 (mp0) cc_final: 0.8356 (mp0) REVERT: T 169 GLU cc_start: 0.8562 (mp0) cc_final: 0.8155 (mp0) REVERT: U 104 ASP cc_start: 0.8750 (m-30) cc_final: 0.8510 (m-30) REVERT: V 19 ARG cc_start: 0.8336 (mpp80) cc_final: 0.7574 (mpp80) REVERT: V 53 PRO cc_start: 0.6005 (Cg_endo) cc_final: 0.5702 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6828 (mmp80) cc_final: 0.6004 (ptp-170) REVERT: V 62 MET cc_start: 0.8164 (ttm) cc_final: 0.7901 (ttm) REVERT: V 96 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8078 (pt0) REVERT: V 155 HIS cc_start: 0.4968 (OUTLIER) cc_final: 0.4504 (m170) REVERT: W 17 MET cc_start: 0.5491 (mpp) cc_final: 0.4321 (ttt) REVERT: W 78 ASN cc_start: 0.8500 (t0) cc_final: 0.7785 (t0) outliers start: 149 outliers final: 108 residues processed: 528 average time/residue: 0.1560 time to fit residues: 125.2031 Evaluate side-chains 516 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 400 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 112 TRP Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 69 ASP Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 19 ILE Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain V residue 26 GLU Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 151 ARG Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 202 ASN Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 208 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 258 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 ASN G 78 ASN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS W 40 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.118472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.095997 restraints weight = 81169.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.098748 restraints weight = 53951.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.100786 restraints weight = 40136.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.102189 restraints weight = 32194.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.103299 restraints weight = 27286.612| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.8215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22444 Z= 0.222 Angle : 0.827 12.176 30566 Z= 0.416 Chirality : 0.052 0.272 3753 Planarity : 0.007 0.059 3918 Dihedral : 5.850 54.918 3090 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 6.60 % Allowed : 30.28 % Favored : 63.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.25 (0.16), residues: 2862 helix: 1.04 (0.16), residues: 1011 sheet: -0.74 (0.18), residues: 759 loop : -0.75 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 179 TYR 0.024 0.002 TYR G 109 PHE 0.048 0.003 PHE E 115 TRP 0.020 0.002 TRP A 112 HIS 0.038 0.003 HIS V 155 Details of bonding type rmsd covalent geometry : bond 0.00513 (22444) covalent geometry : angle 0.82674 (30566) hydrogen bonds : bond 0.05097 ( 1096) hydrogen bonds : angle 4.96911 ( 3153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 398 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7546 (mmm160) cc_final: 0.7268 (mmm160) REVERT: A 94 ILE cc_start: 0.5428 (mm) cc_final: 0.5137 (mm) REVERT: B 199 LEU cc_start: 0.9445 (pp) cc_final: 0.8922 (tp) REVERT: C 54 LYS cc_start: 0.9085 (ttpp) cc_final: 0.8695 (ttpp) REVERT: D 24 ILE cc_start: 0.9155 (mp) cc_final: 0.8468 (tt) REVERT: D 62 MET cc_start: 0.7181 (ptp) cc_final: 0.6949 (ptt) REVERT: D 68 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8445 (tp30) REVERT: E 115 PHE cc_start: 0.7587 (t80) cc_final: 0.7326 (t80) REVERT: F 90 ASP cc_start: 0.7851 (m-30) cc_final: 0.7554 (m-30) REVERT: F 159 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7843 (tpp80) REVERT: G 17 MET cc_start: 0.4219 (ttt) cc_final: 0.3828 (tpp) REVERT: G 36 LYS cc_start: 0.9266 (mmtm) cc_final: 0.8840 (tptp) REVERT: G 77 GLU cc_start: 0.8856 (mp0) cc_final: 0.8530 (pm20) REVERT: I 85 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.6499 (m-80) REVERT: J 19 ARG cc_start: 0.8900 (mpt-90) cc_final: 0.8476 (mpp80) REVERT: J 58 ARG cc_start: 0.6908 (mmp-170) cc_final: 0.6647 (mmp80) REVERT: J 62 MET cc_start: 0.6016 (OUTLIER) cc_final: 0.5470 (tpp) REVERT: J 74 MET cc_start: 0.8492 (mmm) cc_final: 0.8197 (mmp) REVERT: J 142 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7654 (mm) REVERT: J 170 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.5658 (t70) REVERT: N 61 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8676 (mp) REVERT: N 68 GLU cc_start: 0.9236 (mp0) cc_final: 0.8181 (tm-30) REVERT: N 137 ASP cc_start: 0.8858 (t0) cc_final: 0.8510 (t0) REVERT: O 17 MET cc_start: 0.5335 (mmm) cc_final: 0.5125 (mmm) REVERT: Q 17 MET cc_start: 0.6660 (tmm) cc_final: 0.6431 (tpt) REVERT: R 42 LYS cc_start: 0.8840 (mmmt) cc_final: 0.8574 (mmmt) REVERT: R 58 ARG cc_start: 0.7645 (mmp-170) cc_final: 0.7207 (mmp80) REVERT: R 69 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7855 (t70) REVERT: R 72 LYS cc_start: 0.8467 (ptmt) cc_final: 0.8241 (pttp) REVERT: T 18 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7135 (mt-10) REVERT: T 69 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.6919 (t0) REVERT: T 167 ASP cc_start: 0.9178 (OUTLIER) cc_final: 0.8605 (t0) REVERT: T 169 GLU cc_start: 0.8574 (mp0) cc_final: 0.8177 (mp0) REVERT: U 35 LYS cc_start: 0.9255 (tptm) cc_final: 0.9052 (tptm) REVERT: U 42 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9226 (tp) REVERT: U 104 ASP cc_start: 0.8718 (m-30) cc_final: 0.8459 (m-30) REVERT: V 19 ARG cc_start: 0.8344 (mpp80) cc_final: 0.7689 (mpp80) REVERT: V 53 PRO cc_start: 0.6356 (Cg_endo) cc_final: 0.6042 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6900 (mmp80) cc_final: 0.6061 (ptp-170) REVERT: V 68 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8993 (mm-30) REVERT: V 96 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7874 (pm20) REVERT: V 155 HIS cc_start: 0.5041 (OUTLIER) cc_final: 0.4649 (m90) REVERT: W 17 MET cc_start: 0.5419 (mpp) cc_final: 0.4191 (ttt) REVERT: W 40 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7733 (m110) REVERT: W 78 ASN cc_start: 0.8657 (t0) cc_final: 0.7883 (t0) outliers start: 155 outliers final: 117 residues processed: 504 average time/residue: 0.1598 time to fit residues: 123.0578 Evaluate side-chains 505 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 376 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 112 TRP Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 69 ASP Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 19 ILE Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 97 ILE Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 167 ASP Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain V residue 26 GLU Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 151 ARG Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 202 ASN Chi-restraints excluded: chain W residue 40 ASN Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 213 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 chunk 84 optimal weight: 40.0000 chunk 260 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 44 optimal weight: 0.0980 chunk 182 optimal weight: 9.9990 chunk 13 optimal weight: 0.0030 overall best weight: 4.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 202 ASN ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 155 HIS V 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.119705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.097217 restraints weight = 81380.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.100009 restraints weight = 53864.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.102079 restraints weight = 39918.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.103565 restraints weight = 31891.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.104700 restraints weight = 26814.772| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.8404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22444 Z= 0.170 Angle : 0.784 10.867 30566 Z= 0.389 Chirality : 0.050 0.327 3753 Planarity : 0.006 0.056 3918 Dihedral : 5.683 55.607 3090 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.71 % Allowed : 30.66 % Favored : 63.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.16 (0.16), residues: 2862 helix: 1.22 (0.16), residues: 1011 sheet: -0.66 (0.19), residues: 747 loop : -0.83 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 179 TYR 0.023 0.002 TYR G 109 PHE 0.045 0.004 PHE M 115 TRP 0.016 0.002 TRP A 112 HIS 0.017 0.002 HIS V 155 Details of bonding type rmsd covalent geometry : bond 0.00402 (22444) covalent geometry : angle 0.78384 (30566) hydrogen bonds : bond 0.04484 ( 1096) hydrogen bonds : angle 4.78308 ( 3153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 409 time to evaluate : 0.939 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 32 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ARG cc_start: 0.7844 (mmp80) cc_final: 0.7399 (mmp80) REVERT: B 116 ASP cc_start: 0.8197 (t0) cc_final: 0.7648 (p0) REVERT: B 199 LEU cc_start: 0.9426 (pp) cc_final: 0.8856 (tp) REVERT: C 54 LYS cc_start: 0.9100 (ttpp) cc_final: 0.8726 (ttpp) REVERT: D 24 ILE cc_start: 0.9186 (mp) cc_final: 0.8462 (tt) REVERT: D 62 MET cc_start: 0.7309 (ptp) cc_final: 0.7041 (ptt) REVERT: E 115 PHE cc_start: 0.7695 (t80) cc_final: 0.7466 (t80) REVERT: F 90 ASP cc_start: 0.7740 (m-30) cc_final: 0.7425 (m-30) REVERT: F 173 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8691 (pttt) REVERT: G 17 MET cc_start: 0.4626 (ttt) cc_final: 0.3278 (tpt) REVERT: G 36 LYS cc_start: 0.9231 (mmtm) cc_final: 0.8844 (tptp) REVERT: G 37 LEU cc_start: 0.9528 (tt) cc_final: 0.9245 (mp) REVERT: G 75 GLU cc_start: 0.9047 (tp30) cc_final: 0.8384 (mp0) REVERT: I 85 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6573 (m-80) REVERT: J 19 ARG cc_start: 0.8917 (mpt-90) cc_final: 0.8514 (mpp80) REVERT: J 35 LYS cc_start: 0.9224 (tppt) cc_final: 0.8978 (tppt) REVERT: J 58 ARG cc_start: 0.6947 (mmp-170) cc_final: 0.6671 (mmp80) REVERT: J 62 MET cc_start: 0.5946 (tpp) cc_final: 0.5452 (tpp) REVERT: J 74 MET cc_start: 0.8469 (mmm) cc_final: 0.8189 (mmp) REVERT: J 142 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7580 (mm) REVERT: J 170 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.5746 (t70) REVERT: K 17 MET cc_start: 0.3438 (tpp) cc_final: 0.0798 (pmm) REVERT: L 154 GLU cc_start: 0.5619 (pm20) cc_final: 0.4709 (tt0) REVERT: N 68 GLU cc_start: 0.9232 (mp0) cc_final: 0.8375 (tm-30) REVERT: N 137 ASP cc_start: 0.8789 (t0) cc_final: 0.8585 (t0) REVERT: O 17 MET cc_start: 0.5055 (mmm) cc_final: 0.4811 (mmm) REVERT: O 92 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7162 (t70) REVERT: R 42 LYS cc_start: 0.8893 (mmmt) cc_final: 0.8642 (mmmt) REVERT: R 58 ARG cc_start: 0.7637 (mmp-170) cc_final: 0.7191 (mmp80) REVERT: R 69 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7865 (t70) REVERT: R 72 LYS cc_start: 0.8492 (ptmt) cc_final: 0.8263 (pttp) REVERT: T 18 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7391 (mt-10) REVERT: T 69 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6909 (t0) REVERT: T 169 GLU cc_start: 0.8605 (mp0) cc_final: 0.8166 (mp0) REVERT: U 104 ASP cc_start: 0.8698 (m-30) cc_final: 0.8449 (m-30) REVERT: V 19 ARG cc_start: 0.8321 (mpp80) cc_final: 0.7607 (mpp80) REVERT: V 53 PRO cc_start: 0.6476 (Cg_endo) cc_final: 0.6139 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6949 (mmp80) cc_final: 0.6116 (ptp-170) REVERT: V 68 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8988 (mm-30) REVERT: V 159 ARG cc_start: 0.7434 (tpp80) cc_final: 0.7156 (tpp80) REVERT: W 17 MET cc_start: 0.5664 (mpp) cc_final: 0.4402 (ttt) REVERT: W 40 ASN cc_start: 0.8178 (m-40) cc_final: 0.7976 (m-40) REVERT: W 78 ASN cc_start: 0.8640 (t0) cc_final: 0.7887 (t0) outliers start: 134 outliers final: 114 residues processed: 498 average time/residue: 0.1517 time to fit residues: 115.8204 Evaluate side-chains 504 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 382 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 112 TRP Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 69 ASP Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 19 ILE Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 97 ILE Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 151 ARG Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 202 ASN Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 26 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 174 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 chunk 238 optimal weight: 9.9990 chunk 268 optimal weight: 6.9990 chunk 245 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 ASN ** Q 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.120030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.097281 restraints weight = 81430.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.100172 restraints weight = 53669.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.102223 restraints weight = 39814.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.103690 restraints weight = 31924.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.104823 restraints weight = 27011.069| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.8674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22444 Z= 0.167 Angle : 0.781 10.795 30566 Z= 0.387 Chirality : 0.050 0.275 3753 Planarity : 0.006 0.055 3918 Dihedral : 5.619 57.232 3090 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.62 % Allowed : 30.83 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.23 (0.16), residues: 2862 helix: 1.17 (0.16), residues: 1011 sheet: -0.66 (0.19), residues: 747 loop : -0.92 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 179 TYR 0.024 0.002 TYR G 109 PHE 0.046 0.003 PHE E 115 TRP 0.016 0.002 TRP A 112 HIS 0.010 0.001 HIS Q 90 Details of bonding type rmsd covalent geometry : bond 0.00394 (22444) covalent geometry : angle 0.78080 (30566) hydrogen bonds : bond 0.04432 ( 1096) hydrogen bonds : angle 4.74528 ( 3153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 414 time to evaluate : 0.900 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 32 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7628 (mmm160) cc_final: 0.7359 (mmm-85) REVERT: B 58 ARG cc_start: 0.7842 (mmp80) cc_final: 0.7396 (mmp80) REVERT: B 116 ASP cc_start: 0.8209 (t0) cc_final: 0.7704 (p0) REVERT: C 54 LYS cc_start: 0.9033 (ttpp) cc_final: 0.8702 (ttpp) REVERT: C 75 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: D 24 ILE cc_start: 0.9175 (mp) cc_final: 0.8229 (tt) REVERT: D 62 MET cc_start: 0.7408 (ptp) cc_final: 0.7129 (ptt) REVERT: E 115 PHE cc_start: 0.7835 (t80) cc_final: 0.7624 (t80) REVERT: F 90 ASP cc_start: 0.7749 (m-30) cc_final: 0.7463 (m-30) REVERT: F 173 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8702 (pttt) REVERT: G 17 MET cc_start: 0.4785 (ttt) cc_final: 0.4302 (tpt) REVERT: G 36 LYS cc_start: 0.9213 (mmtm) cc_final: 0.8857 (tptp) REVERT: G 37 LEU cc_start: 0.9536 (tt) cc_final: 0.9249 (mp) REVERT: I 85 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.6576 (m-80) REVERT: J 19 ARG cc_start: 0.8908 (mpt-90) cc_final: 0.8548 (mpp80) REVERT: J 35 LYS cc_start: 0.9235 (tppt) cc_final: 0.8979 (tppt) REVERT: J 58 ARG cc_start: 0.6920 (mmp-170) cc_final: 0.6650 (mmp80) REVERT: J 62 MET cc_start: 0.5952 (tpp) cc_final: 0.5430 (tpp) REVERT: J 74 MET cc_start: 0.8472 (mmm) cc_final: 0.8186 (mmp) REVERT: J 142 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7569 (mm) REVERT: J 170 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.5834 (t70) REVERT: K 17 MET cc_start: 0.3663 (tpp) cc_final: 0.1240 (pmm) REVERT: L 154 GLU cc_start: 0.5653 (pm20) cc_final: 0.4890 (tt0) REVERT: M 17 MET cc_start: 0.1091 (OUTLIER) cc_final: 0.0891 (ptm) REVERT: N 68 GLU cc_start: 0.9246 (mp0) cc_final: 0.8415 (tm-30) REVERT: N 79 ASP cc_start: 0.9273 (t0) cc_final: 0.8952 (t0) REVERT: N 137 ASP cc_start: 0.8763 (t0) cc_final: 0.8409 (t0) REVERT: Q 22 THR cc_start: 0.5742 (OUTLIER) cc_final: 0.5529 (p) REVERT: R 42 LYS cc_start: 0.8944 (mmmt) cc_final: 0.8673 (mmmt) REVERT: R 58 ARG cc_start: 0.7675 (mmp-170) cc_final: 0.7202 (mmp80) REVERT: R 69 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7884 (t70) REVERT: R 72 LYS cc_start: 0.8513 (ptmt) cc_final: 0.8269 (pttp) REVERT: S 17 MET cc_start: 0.2353 (mpp) cc_final: 0.0780 (mtp) REVERT: T 18 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7482 (mt-10) REVERT: T 69 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6849 (t0) REVERT: T 167 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8545 (t0) REVERT: T 169 GLU cc_start: 0.8631 (mp0) cc_final: 0.8204 (mp0) REVERT: U 104 ASP cc_start: 0.8696 (m-30) cc_final: 0.8471 (m-30) REVERT: V 53 PRO cc_start: 0.6571 (Cg_endo) cc_final: 0.6220 (Cg_exo) REVERT: V 58 ARG cc_start: 0.7010 (mmp80) cc_final: 0.6208 (ptp-170) REVERT: V 68 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.9025 (mm-30) REVERT: V 151 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6770 (ptm160) REVERT: V 159 ARG cc_start: 0.7380 (tpp80) cc_final: 0.7125 (tpp80) REVERT: W 17 MET cc_start: 0.5754 (mpp) cc_final: 0.4517 (ttt) REVERT: W 78 ASN cc_start: 0.8634 (t0) cc_final: 0.7894 (t0) outliers start: 132 outliers final: 104 residues processed: 502 average time/residue: 0.1640 time to fit residues: 126.6354 Evaluate side-chains 505 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 389 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 112 TRP Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 69 ASP Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 19 ILE Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 167 ASP Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 151 ARG Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 202 ASN Chi-restraints excluded: chain W residue 33 ILE Chi-restraints excluded: chain W residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 214 optimal weight: 0.9990 chunk 229 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 263 optimal weight: 0.1980 chunk 4 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS W 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.119405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.096621 restraints weight = 81302.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.099466 restraints weight = 54005.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.101526 restraints weight = 40160.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.103022 restraints weight = 32195.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.104151 restraints weight = 27204.242| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.8870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22444 Z= 0.165 Angle : 0.803 15.377 30566 Z= 0.394 Chirality : 0.050 0.262 3753 Planarity : 0.006 0.054 3918 Dihedral : 5.595 58.024 3090 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.41 % Allowed : 31.86 % Favored : 62.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 aren not related in a simple way. whole: -0.28 (0.16), residues: 2862 helix: 1.08 (0.16), residues: 1023 sheet: -0.64 (0.19), residues: 747 loop : -0.96 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 179 TYR 0.023 0.002 TYR G 109 PHE 0.040 0.003 PHE E 115 TRP 0.015 0.002 TRP A 112 HIS 0.011 0.001 HIS Q 90 Details of bonding type rmsd covalent geometry : bond 0.00390 (22444) covalent geometry : angle 0.80270 (30566) hydrogen bonds : bond 0.04389 ( 1096) hydrogen bonds : angle 4.71353 ( 3153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4265.01 seconds wall clock time: 74 minutes 17.89 seconds (4457.89 seconds total)