Starting phenix.real_space_refine on Wed May 21 16:59:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8un1_42390/05_2025/8un1_42390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8un1_42390/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8un1_42390/05_2025/8un1_42390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8un1_42390/05_2025/8un1_42390.map" model { file = "/net/cci-nas-00/data/ceres_data/8un1_42390/05_2025/8un1_42390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8un1_42390/05_2025/8un1_42390.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.27, per 1000 atoms: 0.60 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: 5.57 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 2.71 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: 7.78 Time building geometry restraints manager: 6.41 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: 0.650 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: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 49.980 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.040 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.002 TRP C 112 HIS 0.004 0.001 HIS W 90 PHE 0.021 0.004 PHE G 115 TYR 0.030 0.003 TYR C 109 ARG 0.008 0.001 ARG L 179 Details of bonding type rmsd hydrogen bonds : bond 0.19584 ( 1096) hydrogen bonds : angle 6.76464 ( 3153) covalent geometry : bond 0.01440 (22444) covalent geometry : angle 1.16825 (30566) *********************** 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 : 2.717 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7076 (tt0) cc_final: 0.6620 (tm-30) REVERT: A 62 ILE cc_start: 0.7990 (mm) cc_final: 0.7582 (mm) REVERT: A 63 LYS cc_start: 0.7203 (mmtt) cc_final: 0.6860 (mmpt) REVERT: B 62 MET cc_start: 0.8307 (tpp) cc_final: 0.8058 (mmp) REVERT: B 199 LEU cc_start: 0.9199 (pp) cc_final: 0.8908 (tp) REVERT: C 102 PRO cc_start: 0.5747 (Cg_endo) cc_final: 0.5459 (Cg_endo) REVERT: D 75 ILE cc_start: 0.8811 (mm) cc_final: 0.8292 (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: 0.8646 (mttt) 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: 0.7865 (pm20) REVERT: F 58 ARG cc_start: 0.7137 (mmp-170) cc_final: 0.6286 (mmm-85) REVERT: G 72 LEU cc_start: 0.8905 (mp) cc_final: 0.8652 (mp) REVERT: G 101 THR cc_start: 0.5163 (p) cc_final: 0.4609 (p) REVERT: I 42 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6479 (tp) REVERT: I 92 ASP cc_start: 0.7800 (m-30) cc_final: 0.6732 (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: 0.2732 (ptm) REVERT: M 87 LYS cc_start: 0.8852 (tptt) cc_final: 0.8566 (tttm) REVERT: M 97 ILE cc_start: 0.8333 (pt) cc_final: 0.8098 (pt) REVERT: N 26 GLU cc_start: 0.5822 (tm-30) cc_final: 0.5356 (tp30) REVERT: N 61 ILE cc_start: 0.8171 (tt) cc_final: 0.7812 (mp) REVERT: N 68 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8039 (tp30) REVERT: O 116 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7300 (mm-30) REVERT: Q 19 ILE cc_start: 0.7772 (mm) cc_final: 0.7393 (mm) REVERT: R 58 ARG cc_start: 0.7682 (mmp-170) cc_final: 0.7219 (mmp-170) REVERT: T 24 ILE cc_start: 0.7981 (mp) cc_final: 0.7670 (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: 0.6855 (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: 0.7107 (tp) REVERT: W 78 ASN cc_start: 0.8598 (t0) cc_final: 0.7925 (t0) outliers start: 11 outliers final: 3 residues processed: 996 average time/residue: 0.3882 time to fit residues: 559.4838 Evaluate side-chains 542 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 538 time to evaluate : 3.221 ------------------------------------------------------------------------------- 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 238 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 256 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN E 59 ASN K 59 ASN O 59 ASN O 78 ASN ** Q 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.131910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.108647 restraints weight = 80195.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.111701 restraints weight = 53497.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.113927 restraints weight = 39708.089| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 22444 Z= 0.212 Angle : 0.887 9.835 30566 Z= 0.445 Chirality : 0.054 0.323 3753 Planarity : 0.007 0.077 3918 Dihedral : 6.078 58.818 3094 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 7.79 % Allowed : 25.72 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2862 helix: 0.72 (0.15), residues: 1023 sheet: -0.97 (0.17), residues: 888 loop : -0.69 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 112 HIS 0.006 0.001 HIS F 155 PHE 0.025 0.004 PHE O 115 TYR 0.034 0.003 TYR G 109 ARG 0.011 0.001 ARG N 179 Details of bonding type rmsd hydrogen bonds : bond 0.05516 ( 1096) hydrogen bonds : angle 5.19616 ( 3153) covalent geometry : bond 0.00512 (22444) covalent geometry : angle 0.88691 (30566) *********************** 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 751 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 568 time to evaluate : 2.687 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: 0.5428 (mm) cc_final: 0.4967 (mm) REVERT: B 24 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6496 (tp) REVERT: B 69 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7091 (t0) REVERT: B 199 LEU cc_start: 0.9250 (pp) cc_final: 0.8927 (tp) REVERT: C 54 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8391 (ttpp) REVERT: C 55 ILE cc_start: 0.9188 (mm) cc_final: 0.8862 (tp) REVERT: D 24 ILE cc_start: 0.8901 (mp) cc_final: 0.8392 (tt) REVERT: D 52 GLU cc_start: 0.5098 (OUTLIER) cc_final: 0.4661 (pm20) REVERT: D 60 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8054 (tp) REVERT: D 90 ASP cc_start: 0.7805 (t0) cc_final: 0.7525 (t0) REVERT: E 36 LYS cc_start: 0.8596 (mmtm) cc_final: 0.8341 (tptp) REVERT: E 76 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8158 (mm-30) REVERT: E 77 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7575 (tm-30) REVERT: F 69 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.6329 (t0) REVERT: G 23 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8867 (m) REVERT: G 75 GLU cc_start: 0.6967 (pm20) cc_final: 0.6646 (pm20) REVERT: I 21 GLU cc_start: 0.7706 (tp30) cc_final: 0.7182 (tp30) REVERT: I 42 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6858 (tp) REVERT: I 92 ASP cc_start: 0.7905 (m-30) cc_final: 0.6959 (t70) REVERT: J 24 ILE cc_start: 0.5766 (OUTLIER) cc_final: 0.5212 (mp) REVERT: J 168 LYS cc_start: 0.8377 (mppt) cc_final: 0.8076 (mmmt) REVERT: K 77 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8374 (tp30) REVERT: L 69 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6073 (t70) REVERT: M 33 ILE cc_start: 0.8980 (mt) cc_final: 0.8767 (mm) REVERT: Q 21 GLU cc_start: 0.5960 (tp30) cc_final: 0.5211 (mp0) REVERT: Q 98 ILE cc_start: 0.8279 (mp) cc_final: 0.8073 (mp) REVERT: R 58 ARG cc_start: 0.7714 (mmp-170) cc_final: 0.7265 (mmp80) REVERT: R 69 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7755 (t70) REVERT: S 40 ASN cc_start: 0.8562 (p0) cc_final: 0.8150 (p0) REVERT: T 62 MET cc_start: 0.7512 (tpp) cc_final: 0.6916 (tpp) REVERT: T 69 ASP cc_start: 0.6760 (OUTLIER) cc_final: 0.6316 (t0) REVERT: T 176 ARG cc_start: 0.7630 (ptt90) cc_final: 0.7403 (ttm110) REVERT: V 19 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7400 (mpt-90) REVERT: V 53 PRO cc_start: 0.5533 (Cg_endo) cc_final: 0.5206 (Cg_exo) REVERT: V 60 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6565 (tp) REVERT: V 74 MET cc_start: 0.9345 (mmm) cc_final: 0.9129 (mmm) REVERT: V 168 LYS cc_start: 0.9445 (tttt) cc_final: 0.9225 (tptp) REVERT: V 199 LEU cc_start: 0.7932 (pp) cc_final: 0.7375 (tp) REVERT: W 42 LEU cc_start: 0.7355 (tp) cc_final: 0.6895 (tt) REVERT: W 78 ASN cc_start: 0.8341 (t0) cc_final: 0.7628 (t0) REVERT: W 86 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8885 (pt) outliers start: 183 outliers final: 89 residues processed: 691 average time/residue: 0.3346 time to fit residues: 351.7106 Evaluate side-chains 549 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 447 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET 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 69 ASP Chi-restraints excluded: chain B residue 137 ASP 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 71 THR Chi-restraints excluded: chain C residue 77 GLU 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 37 LEU 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 60 LEU 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 144 ASN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 37 LEU 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 122 ILE 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 K residue 83 VAL Chi-restraints excluded: chain K residue 99 VAL 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 M residue 22 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 78 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 O residue 23 THR 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 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 69 ASP 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 69 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 97 ILE Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain T residue 138 VAL 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 38 ASP 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 94 ILE Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 86 ILE 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 45 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN L 155 HIS M 59 ASN Q 59 ASN ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.128761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.105678 restraints weight = 80208.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.108703 restraints weight = 53458.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.110873 restraints weight = 39698.637| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22444 Z= 0.172 Angle : 0.789 11.875 30566 Z= 0.392 Chirality : 0.051 0.272 3753 Planarity : 0.007 0.089 3918 Dihedral : 5.773 58.596 3092 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 7.50 % Allowed : 26.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2862 helix: 0.87 (0.16), residues: 1023 sheet: -0.87 (0.16), residues: 924 loop : -0.50 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Q 112 HIS 0.031 0.002 HIS V 155 PHE 0.029 0.003 PHE E 115 TYR 0.023 0.002 TYR A 109 ARG 0.006 0.001 ARG V 19 Details of bonding type rmsd hydrogen bonds : bond 0.04923 ( 1096) hydrogen bonds : angle 4.94050 ( 3153) covalent geometry : bond 0.00406 (22444) covalent geometry : angle 0.78944 (30566) *********************** 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 661 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 485 time to evaluate : 2.821 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: A 94 ILE cc_start: 0.5340 (mm) cc_final: 0.4824 (mm) REVERT: A 109 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.7089 (t80) REVERT: B 24 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6665 (mt) REVERT: B 69 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7030 (t0) REVERT: B 199 LEU cc_start: 0.9281 (pp) cc_final: 0.8962 (tp) REVERT: C 49 THR cc_start: 0.8175 (t) cc_final: 0.7843 (p) REVERT: C 54 LYS cc_start: 0.8946 (ttpp) cc_final: 0.8548 (ttpp) REVERT: D 24 ILE cc_start: 0.9089 (mp) cc_final: 0.8469 (tt) REVERT: D 30 TYR cc_start: 0.8078 (t80) cc_final: 0.7854 (t80) REVERT: D 68 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8259 (tp30) REVERT: D 90 ASP cc_start: 0.7865 (t0) cc_final: 0.7615 (t0) REVERT: E 31 LYS cc_start: 0.8558 (mttt) cc_final: 0.8158 (mmmt) REVERT: E 36 LYS cc_start: 0.8400 (mmtm) cc_final: 0.7645 (tptp) REVERT: E 40 ASN cc_start: 0.9206 (OUTLIER) cc_final: 0.8950 (t0) REVERT: E 76 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7883 (mm-30) REVERT: E 115 PHE cc_start: 0.7661 (t80) cc_final: 0.6430 (t80) REVERT: F 69 ASP cc_start: 0.6793 (OUTLIER) cc_final: 0.6542 (t0) REVERT: G 36 LYS cc_start: 0.9341 (mmtm) cc_final: 0.8873 (tptp) REVERT: G 75 GLU cc_start: 0.6863 (pm20) cc_final: 0.5748 (pm20) REVERT: J 24 ILE cc_start: 0.6000 (OUTLIER) cc_final: 0.5756 (tt) REVERT: J 62 MET cc_start: 0.6107 (tpp) cc_final: 0.5845 (tpp) REVERT: J 142 LEU cc_start: 0.6884 (tp) cc_final: 0.5734 (tp) REVERT: K 41 ARG cc_start: 0.8809 (mtp85) cc_final: 0.8609 (mtp85) REVERT: L 179 ARG cc_start: 0.9126 (ttm110) cc_final: 0.8871 (ttm110) REVERT: M 33 ILE cc_start: 0.9090 (mt) cc_final: 0.8861 (mm) REVERT: N 61 ILE cc_start: 0.8779 (tt) cc_final: 0.8498 (mp) REVERT: O 28 GLU cc_start: 0.8602 (pm20) cc_final: 0.8295 (pm20) REVERT: Q 21 GLU cc_start: 0.6090 (tp30) cc_final: 0.5289 (mp0) REVERT: Q 98 ILE cc_start: 0.8394 (mp) cc_final: 0.8182 (mp) REVERT: Q 116 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7282 (tp30) REVERT: R 58 ARG cc_start: 0.7671 (mmp-170) cc_final: 0.7360 (mmp80) REVERT: R 69 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7743 (t70) REVERT: S 21 GLU cc_start: 0.8779 (tp30) cc_final: 0.8353 (tp30) REVERT: T 69 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6380 (t0) REVERT: T 165 ILE cc_start: 0.7275 (OUTLIER) cc_final: 0.7032 (pt) REVERT: V 19 ARG cc_start: 0.7643 (mtm-85) cc_final: 0.7351 (mpp80) REVERT: V 53 PRO cc_start: 0.5726 (Cg_endo) cc_final: 0.5343 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6292 (mmp80) cc_final: 0.5452 (mtt180) REVERT: V 96 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7602 (pt0) REVERT: V 199 LEU cc_start: 0.7916 (pp) cc_final: 0.7393 (tp) REVERT: W 42 LEU cc_start: 0.7596 (tp) cc_final: 0.7111 (tt) REVERT: W 78 ASN cc_start: 0.8382 (t0) cc_final: 0.7657 (t0) REVERT: W 86 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8781 (pt) outliers start: 176 outliers final: 102 residues processed: 598 average time/residue: 0.3515 time to fit residues: 317.3414 Evaluate side-chains 542 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 430 time to evaluate : 2.612 ------------------------------------------------------------------------------- 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 A residue 109 TYR 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 69 ASP Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 191 ILE 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 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 88 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 40 ASN 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 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL 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 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 129 VAL 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 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 187 LEU Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 22 THR 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 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 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 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 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 148 THR 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 T residue 48 LEU 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 165 ILE 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 86 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 97 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 152 LEU 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 31 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 129 optimal weight: 8.9990 chunk 253 optimal weight: 7.9990 chunk 223 optimal weight: 20.0000 chunk 224 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 256 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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 ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 ASN ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 155 HIS R 202 ASN S 78 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.122815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.099634 restraints weight = 80389.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.102547 restraints weight = 53268.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.104630 restraints weight = 39400.534| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 22444 Z= 0.207 Angle : 0.800 10.782 30566 Z= 0.404 Chirality : 0.052 0.290 3753 Planarity : 0.007 0.066 3918 Dihedral : 5.894 56.667 3090 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 8.18 % Allowed : 26.83 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2862 helix: 0.75 (0.16), residues: 1023 sheet: -0.73 (0.17), residues: 792 loop : -0.77 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP Q 112 HIS 0.006 0.001 HIS K 90 PHE 0.038 0.004 PHE Q 115 TYR 0.032 0.002 TYR A 109 ARG 0.011 0.001 ARG J 141 Details of bonding type rmsd hydrogen bonds : bond 0.05139 ( 1096) hydrogen bonds : angle 5.00295 ( 3153) covalent geometry : bond 0.00487 (22444) covalent geometry : angle 0.79990 (30566) *********************** 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 643 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 451 time to evaluate : 2.444 Fit side-chains revert: symmetry clash 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: 0.5600 (mm) cc_final: 0.5077 (mm) REVERT: A 109 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.7219 (t80) REVERT: B 69 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7178 (t0) REVERT: B 74 MET cc_start: 0.8394 (mmm) cc_final: 0.8140 (mmt) REVERT: B 152 LEU cc_start: 0.8777 (mp) cc_final: 0.8546 (mp) REVERT: B 165 ILE cc_start: 0.8086 (pt) cc_final: 0.7758 (pt) REVERT: B 199 LEU cc_start: 0.9385 (pp) cc_final: 0.8983 (tp) REVERT: C 54 LYS cc_start: 0.9055 (ttpp) cc_final: 0.8702 (ttpp) REVERT: D 24 ILE cc_start: 0.9126 (mp) cc_final: 0.8526 (tt) REVERT: D 52 GLU cc_start: 0.4915 (OUTLIER) cc_final: 0.4556 (pm20) REVERT: D 69 ASP cc_start: 0.7448 (m-30) cc_final: 0.7195 (m-30) REVERT: E 31 LYS cc_start: 0.8575 (mttt) cc_final: 0.8199 (mmmt) REVERT: E 36 LYS cc_start: 0.8642 (mmtm) cc_final: 0.7999 (tptp) REVERT: F 25 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8031 (mm) REVERT: F 69 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7173 (t0) REVERT: F 90 ASP cc_start: 0.7984 (m-30) cc_final: 0.7561 (m-30) REVERT: G 36 LYS cc_start: 0.9298 (mmtm) cc_final: 0.8825 (tptp) REVERT: G 77 GLU cc_start: 0.8823 (mp0) cc_final: 0.8355 (pp20) REVERT: I 35 LYS cc_start: 0.9037 (tptp) cc_final: 0.8810 (tptp) REVERT: J 24 ILE cc_start: 0.6371 (OUTLIER) cc_final: 0.6152 (tt) REVERT: J 32 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.7816 (ttp-170) REVERT: J 62 MET cc_start: 0.6376 (tpp) cc_final: 0.5944 (tpp) REVERT: J 63 LEU cc_start: 0.8299 (pt) cc_final: 0.7866 (mp) REVERT: K 17 MET cc_start: 0.3680 (mmm) cc_final: 0.1642 (pmm) REVERT: K 41 ARG cc_start: 0.8850 (mtp85) cc_final: 0.8190 (tpp-160) REVERT: M 33 ILE cc_start: 0.9091 (mt) cc_final: 0.8838 (mm) REVERT: M 52 LEU cc_start: 0.6779 (mm) cc_final: 0.6321 (mp) REVERT: N 61 ILE cc_start: 0.8786 (tt) cc_final: 0.8560 (mp) REVERT: O 28 GLU cc_start: 0.8668 (pm20) cc_final: 0.8457 (pm20) REVERT: Q 116 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7518 (tp30) REVERT: R 58 ARG cc_start: 0.7786 (mmp-170) cc_final: 0.7476 (mmp80) REVERT: R 69 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7853 (t70) REVERT: R 142 LEU cc_start: 0.6686 (tp) cc_final: 0.6449 (tp) REVERT: S 21 GLU cc_start: 0.8663 (tp30) cc_final: 0.8123 (tp30) REVERT: T 69 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6685 (t0) REVERT: V 19 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7446 (mpp80) REVERT: V 53 PRO cc_start: 0.5930 (Cg_endo) cc_final: 0.5541 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6568 (mmp80) cc_final: 0.5725 (ptp-170) REVERT: V 96 GLU cc_start: 0.8662 (mm-30) cc_final: 0.7911 (pt0) REVERT: W 42 LEU cc_start: 0.7683 (tp) cc_final: 0.7458 (pp) REVERT: W 78 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8122 (t0) outliers start: 192 outliers final: 118 residues processed: 580 average time/residue: 0.3329 time to fit residues: 294.4027 Evaluate side-chains 527 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 400 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 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 A residue 109 TYR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 137 ASP 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 43 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 99 VAL 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 88 LEU Chi-restraints excluded: chain D residue 93 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 D residue 150 MET Chi-restraints excluded: chain E residue 23 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 25 LEU Chi-restraints excluded: chain F residue 69 ASP 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 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 109 TYR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 24 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 138 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 46 VAL 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 178 ILE Chi-restraints excluded: chain L residue 187 LEU 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 M residue 86 ILE 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 O residue 23 THR 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 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 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 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 71 THR 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 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 47 ILE Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 100 ILE 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 97 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 142 LEU 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 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 31 LYS Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 78 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 95 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 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** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 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 = 0.4042 r_free = 0.4042 target = 0.123112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.100324 restraints weight = 81514.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.103311 restraints weight = 53373.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.105469 restraints weight = 39246.373| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.7155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 22444 Z= 0.171 Angle : 0.758 11.523 30566 Z= 0.380 Chirality : 0.050 0.250 3753 Planarity : 0.006 0.065 3918 Dihedral : 5.697 57.072 3090 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 7.03 % Allowed : 28.36 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2862 helix: 1.01 (0.16), residues: 1023 sheet: -0.59 (0.18), residues: 747 loop : -0.79 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP Q 112 HIS 0.033 0.002 HIS V 155 PHE 0.021 0.003 PHE E 115 TYR 0.025 0.002 TYR A 109 ARG 0.011 0.001 ARG L 179 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 1096) hydrogen bonds : angle 4.78649 ( 3153) covalent geometry : bond 0.00403 (22444) covalent geometry : angle 0.75772 (30566) *********************** 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 616 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 451 time to evaluate : 2.738 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 58 GLU cc_start: 0.7411 (tt0) cc_final: 0.6927 (tm-30) REVERT: A 109 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.7160 (t80) REVERT: B 69 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7161 (t0) REVERT: B 199 LEU cc_start: 0.9393 (pp) cc_final: 0.8941 (tp) REVERT: C 54 LYS cc_start: 0.9077 (ttpp) cc_final: 0.8644 (ttpp) REVERT: D 24 ILE cc_start: 0.9163 (mp) cc_final: 0.8468 (tt) REVERT: D 52 GLU cc_start: 0.4954 (OUTLIER) cc_final: 0.4692 (pm20) REVERT: D 68 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8170 (tp30) REVERT: D 69 ASP cc_start: 0.7585 (m-30) cc_final: 0.7372 (m-30) REVERT: E 31 LYS cc_start: 0.8516 (mttt) cc_final: 0.8240 (mmmt) REVERT: E 36 LYS cc_start: 0.8736 (mmtm) cc_final: 0.8002 (tptp) REVERT: F 69 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7146 (t0) REVERT: F 90 ASP cc_start: 0.7978 (m-30) cc_final: 0.7533 (m-30) REVERT: G 36 LYS cc_start: 0.9311 (mmtm) cc_final: 0.8911 (tptp) REVERT: I 35 LYS cc_start: 0.9087 (tptp) cc_final: 0.8876 (tptp) REVERT: J 19 ARG cc_start: 0.8810 (mpt-90) cc_final: 0.8378 (mpp80) REVERT: J 24 ILE cc_start: 0.6519 (OUTLIER) cc_final: 0.6313 (tt) REVERT: J 32 ARG cc_start: 0.8507 (mtt-85) cc_final: 0.8124 (ttm-80) REVERT: J 62 MET cc_start: 0.6280 (tpp) cc_final: 0.5802 (tpp) REVERT: K 41 ARG cc_start: 0.8912 (mtp85) cc_final: 0.8254 (tpp-160) REVERT: R 58 ARG cc_start: 0.7609 (mmp-170) cc_final: 0.7164 (mmp80) REVERT: R 69 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7842 (t70) REVERT: S 17 MET cc_start: 0.2918 (OUTLIER) cc_final: 0.2521 (tpp) REVERT: S 21 GLU cc_start: 0.8711 (tp30) cc_final: 0.8240 (tp30) REVERT: T 69 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6775 (t0) REVERT: U 104 ASP cc_start: 0.8689 (m-30) cc_final: 0.8471 (m-30) REVERT: V 19 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.7532 (mpp80) REVERT: V 53 PRO cc_start: 0.6038 (Cg_endo) cc_final: 0.5626 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6704 (mmp80) cc_final: 0.5806 (ptp-170) REVERT: V 96 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8005 (pt0) REVERT: W 78 ASN cc_start: 0.8613 (m-40) cc_final: 0.8188 (t0) outliers start: 165 outliers final: 106 residues processed: 562 average time/residue: 0.3271 time to fit residues: 281.4191 Evaluate side-chains 518 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 404 time to evaluate : 2.600 ------------------------------------------------------------------------------- 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 A residue 109 TYR 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 69 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 137 ASP 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 71 THR Chi-restraints excluded: chain C residue 78 ASN 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 D residue 150 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 39 GLU 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 46 VAL Chi-restraints excluded: chain F residue 69 ASP 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 126 VAL 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 64 SER Chi-restraints excluded: chain G residue 70 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 J residue 24 ILE Chi-restraints excluded: chain J residue 79 ASP 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 156 ILE Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 165 ILE 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 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 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 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 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 148 THR Chi-restraints excluded: chain S residue 17 MET 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 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 127 SER Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 100 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 97 ILE Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 142 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 79 optimal weight: 5.9990 chunk 205 optimal weight: 20.0000 chunk 221 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 255 optimal weight: 8.9990 chunk 182 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 201 optimal weight: 0.0170 chunk 2 optimal weight: 5.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 GLN R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.122740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.099903 restraints weight = 81014.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.102878 restraints weight = 53111.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.105041 restraints weight = 39051.955| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.7572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 22444 Z= 0.159 Angle : 0.743 11.133 30566 Z= 0.370 Chirality : 0.050 0.333 3753 Planarity : 0.006 0.054 3918 Dihedral : 5.467 53.504 3088 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 6.73 % Allowed : 29.51 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2862 helix: 1.14 (0.16), residues: 1023 sheet: -0.52 (0.18), residues: 747 loop : -0.79 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Q 112 HIS 0.005 0.001 HIS T 155 PHE 0.026 0.003 PHE E 115 TYR 0.024 0.002 TYR A 109 ARG 0.011 0.001 ARG L 179 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 1096) hydrogen bonds : angle 4.67546 ( 3153) covalent geometry : bond 0.00378 (22444) covalent geometry : angle 0.74304 (30566) *********************** 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 595 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 437 time to evaluate : 2.516 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 58 GLU cc_start: 0.7511 (tt0) cc_final: 0.6988 (tm-30) REVERT: A 109 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.7175 (t80) REVERT: B 199 LEU cc_start: 0.9449 (pp) cc_final: 0.8985 (tp) REVERT: C 54 LYS cc_start: 0.9128 (ttpp) cc_final: 0.8704 (ttpp) REVERT: D 24 ILE cc_start: 0.9169 (mp) cc_final: 0.8496 (tt) REVERT: D 68 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8297 (tp30) REVERT: D 69 ASP cc_start: 0.7941 (m-30) cc_final: 0.7647 (m-30) REVERT: E 31 LYS cc_start: 0.8541 (mttt) cc_final: 0.8311 (mmmt) REVERT: E 36 LYS cc_start: 0.8794 (mmtm) cc_final: 0.7994 (tptp) REVERT: E 115 PHE cc_start: 0.7205 (t80) cc_final: 0.6740 (t80) REVERT: F 69 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7224 (t0) REVERT: F 90 ASP cc_start: 0.7933 (m-30) cc_final: 0.7578 (m-30) REVERT: F 159 ARG cc_start: 0.7975 (tpp80) cc_final: 0.7506 (tpp80) REVERT: G 17 MET cc_start: 0.4563 (ttt) cc_final: 0.3819 (tpt) REVERT: G 36 LYS cc_start: 0.9296 (mmtm) cc_final: 0.8885 (tptp) REVERT: G 61 GLU cc_start: 0.7829 (mp0) cc_final: 0.7576 (mp0) REVERT: I 35 LYS cc_start: 0.9123 (tptp) cc_final: 0.8863 (tptp) REVERT: I 85 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.6425 (m-80) REVERT: J 19 ARG cc_start: 0.8867 (mpt-90) cc_final: 0.8455 (mpp80) REVERT: J 24 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.6165 (tt) REVERT: J 62 MET cc_start: 0.6239 (tpp) cc_final: 0.5761 (tpp) REVERT: K 17 MET cc_start: 0.3708 (tpp) cc_final: 0.0835 (pmm) REVERT: K 37 LEU cc_start: 0.9035 (tp) cc_final: 0.8697 (mm) REVERT: K 41 ARG cc_start: 0.8931 (mtp85) cc_final: 0.8273 (tpp-160) REVERT: L 26 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6711 (mt-10) REVERT: N 137 ASP cc_start: 0.8912 (t0) cc_final: 0.8371 (t0) REVERT: R 58 ARG cc_start: 0.7754 (mmp-170) cc_final: 0.7296 (mmp80) REVERT: R 62 MET cc_start: 0.7512 (mpp) cc_final: 0.7208 (mpp) REVERT: R 69 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7870 (t70) REVERT: S 17 MET cc_start: 0.2985 (OUTLIER) cc_final: 0.2443 (tpp) REVERT: T 18 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7017 (mt-10) REVERT: T 69 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6800 (t0) REVERT: U 54 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8432 (mmmt) REVERT: V 19 ARG cc_start: 0.8083 (mtm-85) cc_final: 0.7557 (mpp80) REVERT: V 53 PRO cc_start: 0.6134 (Cg_endo) cc_final: 0.5729 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6803 (mmp80) cc_final: 0.5976 (ptp-170) REVERT: V 96 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8009 (pt0) REVERT: W 17 MET cc_start: 0.5233 (OUTLIER) cc_final: 0.4993 (mtm) REVERT: W 78 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8138 (t0) outliers start: 158 outliers final: 117 residues processed: 538 average time/residue: 0.3299 time to fit residues: 268.8868 Evaluate side-chains 525 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 399 time to evaluate : 2.619 ------------------------------------------------------------------------------- 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 98 ILE Chi-restraints excluded: chain A residue 109 TYR 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 17 MET Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 38 ASP 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 D residue 150 MET Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 39 GLU 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 46 VAL Chi-restraints excluded: chain F residue 69 ASP 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 126 VAL 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 109 TYR Chi-restraints excluded: chain I residue 23 THR 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 24 ILE Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 170 ASP 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 121 ILE 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 165 ILE 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 M residue 49 THR Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 122 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 196 VAL Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 99 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 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 S residue 17 MET Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 48 ILE 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 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 196 VAL Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 100 ILE 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 97 ILE Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain W residue 17 MET Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 78 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 235 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 222 optimal weight: 0.0870 chunk 95 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 overall best weight: 3.8166 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 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 98 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 = 0.4016 r_free = 0.4016 target = 0.121540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.098532 restraints weight = 80963.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.101444 restraints weight = 53342.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.103594 restraints weight = 39421.400| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.7925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22444 Z= 0.160 Angle : 0.757 13.064 30566 Z= 0.375 Chirality : 0.050 0.299 3753 Planarity : 0.006 0.054 3918 Dihedral : 5.421 53.803 3088 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.39 % Allowed : 30.37 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2862 helix: 1.16 (0.16), residues: 1035 sheet: -0.45 (0.18), residues: 735 loop : -0.92 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q 112 HIS 0.006 0.001 HIS T 155 PHE 0.026 0.003 PHE M 115 TYR 0.026 0.002 TYR A 109 ARG 0.012 0.001 ARG L 179 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 1096) hydrogen bonds : angle 4.65789 ( 3153) covalent geometry : bond 0.00379 (22444) covalent geometry : angle 0.75698 (30566) *********************** 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 577 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 427 time to evaluate : 2.553 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: A 109 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.7259 (t80) REVERT: A 116 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8175 (mm-30) REVERT: B 58 ARG cc_start: 0.8036 (mmp80) cc_final: 0.7632 (mmm-85) REVERT: B 199 LEU cc_start: 0.9460 (pp) cc_final: 0.8996 (tp) REVERT: C 54 LYS cc_start: 0.9107 (ttpp) cc_final: 0.8686 (ttpp) REVERT: D 24 ILE cc_start: 0.9142 (mp) cc_final: 0.8485 (tt) REVERT: D 68 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8362 (tp30) REVERT: D 69 ASP cc_start: 0.8031 (m-30) cc_final: 0.7756 (m-30) REVERT: D 112 GLU cc_start: 0.3435 (pm20) cc_final: 0.3105 (pm20) REVERT: E 31 LYS cc_start: 0.8517 (mttt) cc_final: 0.8283 (mmmt) REVERT: E 36 LYS cc_start: 0.8858 (mmtm) cc_final: 0.8062 (tptp) REVERT: E 115 PHE cc_start: 0.7268 (t80) cc_final: 0.6896 (t80) REVERT: F 90 ASP cc_start: 0.7873 (m-30) cc_final: 0.7525 (m-30) REVERT: F 159 ARG cc_start: 0.7975 (tpp80) cc_final: 0.7696 (tpp80) REVERT: G 17 MET cc_start: 0.4575 (ttt) cc_final: 0.3985 (tpt) REVERT: G 61 GLU cc_start: 0.7900 (mp0) cc_final: 0.7624 (mp0) REVERT: I 35 LYS cc_start: 0.9118 (tptp) cc_final: 0.8879 (tptp) REVERT: I 85 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.6413 (m-80) REVERT: J 19 ARG cc_start: 0.8929 (mpt-90) cc_final: 0.8523 (mpp80) REVERT: J 24 ILE cc_start: 0.6417 (OUTLIER) cc_final: 0.6197 (tt) REVERT: J 32 ARG cc_start: 0.8616 (mtt-85) cc_final: 0.8150 (ttm-80) REVERT: J 35 LYS cc_start: 0.9198 (tppt) cc_final: 0.8966 (tppt) REVERT: J 58 ARG cc_start: 0.6905 (mmp-170) cc_final: 0.6594 (mmp80) REVERT: J 62 MET cc_start: 0.6255 (tpp) cc_final: 0.5781 (tpp) REVERT: K 17 MET cc_start: 0.3915 (tpp) cc_final: 0.1004 (pmm) REVERT: K 37 LEU cc_start: 0.9048 (tp) cc_final: 0.8836 (mm) REVERT: K 41 ARG cc_start: 0.8908 (mtp85) cc_final: 0.8358 (ptm-80) REVERT: L 26 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7007 (mt-10) REVERT: L 154 GLU cc_start: 0.5927 (pm20) cc_final: 0.5266 (mt-10) REVERT: M 52 LEU cc_start: 0.7940 (mp) cc_final: 0.7648 (mp) REVERT: N 137 ASP cc_start: 0.8866 (t0) cc_final: 0.8340 (t0) REVERT: O 69 ARG cc_start: 0.8547 (tmm-80) cc_final: 0.8303 (tmm-80) REVERT: R 58 ARG cc_start: 0.7761 (mmp-170) cc_final: 0.7241 (mmp80) REVERT: T 18 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7208 (mt-10) REVERT: T 69 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6889 (t0) REVERT: T 167 ASP cc_start: 0.9001 (t0) cc_final: 0.8649 (t0) REVERT: T 169 GLU cc_start: 0.8662 (mp0) cc_final: 0.8231 (mp0) REVERT: V 19 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7623 (mpp80) REVERT: V 53 PRO cc_start: 0.6303 (Cg_endo) cc_final: 0.5913 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6942 (mmp80) cc_final: 0.6083 (ptp-170) REVERT: V 62 MET cc_start: 0.8206 (ttm) cc_final: 0.7950 (ttm) REVERT: V 96 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8044 (pt0) REVERT: W 69 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.8163 (ttm-80) REVERT: W 78 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8147 (t0) outliers start: 150 outliers final: 120 residues processed: 527 average time/residue: 0.3422 time to fit residues: 273.6551 Evaluate side-chains 527 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 402 time to evaluate : 2.792 ------------------------------------------------------------------------------- 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 A residue 109 TYR 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 89 ILE 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 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 38 ASP 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 D residue 150 MET Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 39 GLU 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 126 VAL Chi-restraints excluded: chain F residue 144 ASN 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 70 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 23 THR 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 24 ILE Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 71 THR 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 L residue 165 ILE 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 M residue 86 ILE Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 122 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 196 VAL Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 99 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 99 VAL 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 S residue 17 MET 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 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 U residue 22 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 100 ILE 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 97 ILE Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 129 VAL 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 17 MET Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 78 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 260 optimal weight: 8.9990 chunk 239 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 210 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 252 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 277 optimal weight: 7.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 202 ASN ** N 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.122608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.099672 restraints weight = 80524.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.102630 restraints weight = 53247.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.104780 restraints weight = 39342.196| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.8111 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= 0.140 Angle : 0.738 10.533 30566 Z= 0.362 Chirality : 0.049 0.326 3753 Planarity : 0.006 0.052 3918 Dihedral : 5.248 54.204 3088 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.41 % Allowed : 32.03 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2862 helix: 1.34 (0.16), residues: 1035 sheet: -0.39 (0.18), residues: 735 loop : -0.96 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 112 HIS 0.006 0.001 HIS T 155 PHE 0.026 0.003 PHE M 115 TYR 0.023 0.001 TYR A 109 ARG 0.012 0.001 ARG L 179 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 1096) hydrogen bonds : angle 4.51129 ( 3153) covalent geometry : bond 0.00330 (22444) covalent geometry : angle 0.73773 (30566) *********************** 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 562 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 435 time to evaluate : 2.443 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 109 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.7347 (t80) REVERT: A 116 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8007 (mm-30) REVERT: B 62 MET cc_start: 0.8683 (tpp) cc_final: 0.8477 (mmm) REVERT: B 199 LEU cc_start: 0.9457 (pp) cc_final: 0.9000 (tp) REVERT: C 54 LYS cc_start: 0.9124 (ttpp) cc_final: 0.8642 (ttpp) REVERT: D 24 ILE cc_start: 0.9056 (mp) cc_final: 0.8448 (tt) REVERT: D 68 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8379 (tp30) REVERT: D 69 ASP cc_start: 0.8021 (m-30) cc_final: 0.7735 (m-30) REVERT: D 115 LYS cc_start: 0.7873 (mptt) cc_final: 0.7658 (mmtt) REVERT: E 31 LYS cc_start: 0.8515 (mttt) cc_final: 0.8281 (mmmt) REVERT: E 36 LYS cc_start: 0.8874 (mmtm) cc_final: 0.8074 (tptp) REVERT: E 115 PHE cc_start: 0.7425 (t80) cc_final: 0.7136 (t80) REVERT: F 90 ASP cc_start: 0.7834 (m-30) cc_final: 0.7487 (m-30) REVERT: F 159 ARG cc_start: 0.7932 (tpp80) cc_final: 0.7656 (tpp80) REVERT: G 17 MET cc_start: 0.4549 (ttt) cc_final: 0.4034 (tpt) REVERT: G 61 GLU cc_start: 0.7885 (mp0) cc_final: 0.7597 (mp0) REVERT: I 35 LYS cc_start: 0.9116 (tptp) cc_final: 0.8876 (tptp) REVERT: I 85 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6343 (m-80) REVERT: J 19 ARG cc_start: 0.8951 (mpt-90) cc_final: 0.8561 (mpp80) REVERT: J 58 ARG cc_start: 0.6939 (mmp-170) cc_final: 0.6651 (mmp80) REVERT: J 62 MET cc_start: 0.6186 (tpp) cc_final: 0.5787 (tpp) REVERT: J 102 LEU cc_start: 0.8883 (mp) cc_final: 0.8160 (tt) REVERT: K 17 MET cc_start: 0.3843 (tpp) cc_final: 0.1498 (pmm) REVERT: K 37 LEU cc_start: 0.9139 (tp) cc_final: 0.8856 (mm) REVERT: K 41 ARG cc_start: 0.8954 (mtp85) cc_final: 0.8531 (ptm-80) REVERT: L 26 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7056 (mt-10) REVERT: L 154 GLU cc_start: 0.6125 (pm20) cc_final: 0.5378 (tt0) REVERT: M 17 MET cc_start: 0.1647 (OUTLIER) cc_final: 0.1368 (ptm) REVERT: M 45 GLU cc_start: 0.7948 (tp30) cc_final: 0.7601 (tt0) REVERT: M 52 LEU cc_start: 0.7907 (mp) cc_final: 0.7538 (mp) REVERT: M 73 TYR cc_start: 0.8085 (m-80) cc_final: 0.7717 (m-80) REVERT: N 137 ASP cc_start: 0.8845 (t0) cc_final: 0.8368 (t0) REVERT: N 150 MET cc_start: 0.8526 (pmm) cc_final: 0.8071 (pmm) REVERT: O 69 ARG cc_start: 0.8552 (tmm-80) cc_final: 0.8321 (tmm-80) REVERT: O 92 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6737 (t70) REVERT: R 58 ARG cc_start: 0.7727 (mmp-170) cc_final: 0.7235 (mmp80) REVERT: R 72 LYS cc_start: 0.8479 (ptmt) cc_final: 0.8224 (pttt) REVERT: S 17 MET cc_start: 0.3442 (OUTLIER) cc_final: 0.2852 (mmm) REVERT: T 18 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7315 (mt-10) REVERT: T 69 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6801 (t0) REVERT: T 167 ASP cc_start: 0.8988 (t0) cc_final: 0.8619 (t0) REVERT: T 169 GLU cc_start: 0.8677 (mp0) cc_final: 0.8236 (mp0) REVERT: V 19 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7600 (mpp80) REVERT: V 53 PRO cc_start: 0.6431 (Cg_endo) cc_final: 0.6072 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6994 (mmp80) cc_final: 0.6128 (ptp-170) REVERT: V 96 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8037 (pt0) REVERT: V 159 ARG cc_start: 0.7433 (tpp80) cc_final: 0.7131 (tpp80) REVERT: W 69 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.8203 (ttm-80) REVERT: W 78 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8011 (t0) outliers start: 127 outliers final: 98 residues processed: 521 average time/residue: 0.3208 time to fit residues: 255.6353 Evaluate side-chains 519 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 414 time to evaluate : 2.707 ------------------------------------------------------------------------------- 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 A residue 109 TYR 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 B residue 202 ASN Chi-restraints excluded: chain C residue 24 THR 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 38 ASP 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 D residue 150 MET Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 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 70 VAL 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 144 ASN 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 71 THR Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 79 ASP 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 156 ILE Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain L residue 121 ILE 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 165 ILE 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 122 ILE 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 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 99 VAL Chi-restraints excluded: chain R residue 41 LEU 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 S residue 17 MET 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 69 ASP Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 47 ILE 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 156 ILE Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain W residue 78 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 90 optimal weight: 0.3980 chunk 56 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 247 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.121522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.098668 restraints weight = 81656.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.101627 restraints weight = 53752.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.103759 restraints weight = 39707.845| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.8421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22444 Z= 0.155 Angle : 0.747 10.145 30566 Z= 0.369 Chirality : 0.049 0.284 3753 Planarity : 0.006 0.065 3918 Dihedral : 5.294 54.727 3088 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.20 % Allowed : 32.24 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2862 helix: 1.28 (0.16), residues: 1035 sheet: -0.38 (0.19), residues: 729 loop : -1.01 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 112 HIS 0.006 0.001 HIS T 155 PHE 0.029 0.003 PHE M 115 TYR 0.025 0.002 TYR A 109 ARG 0.014 0.001 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 1096) hydrogen bonds : angle 4.59423 ( 3153) covalent geometry : bond 0.00368 (22444) covalent geometry : angle 0.74667 (30566) *********************** 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 553 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 431 time to evaluate : 2.707 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: 0.6971 (mmm160) cc_final: 0.6586 (mmm160) REVERT: A 109 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7308 (t80) REVERT: B 58 ARG cc_start: 0.7954 (mmp80) cc_final: 0.7650 (mtp85) REVERT: B 62 MET cc_start: 0.8598 (tpp) cc_final: 0.8391 (mmm) REVERT: C 54 LYS cc_start: 0.9132 (ttpp) cc_final: 0.8653 (ttpp) REVERT: D 24 ILE cc_start: 0.9134 (mp) cc_final: 0.8509 (tt) REVERT: D 69 ASP cc_start: 0.8133 (m-30) cc_final: 0.7832 (m-30) REVERT: E 31 LYS cc_start: 0.8518 (mttt) cc_final: 0.8306 (mmmt) REVERT: E 115 PHE cc_start: 0.7524 (t80) cc_final: 0.7240 (t80) REVERT: F 90 ASP cc_start: 0.7934 (m-30) cc_final: 0.7586 (m-30) REVERT: F 159 ARG cc_start: 0.7986 (tpp80) cc_final: 0.7714 (tpp80) REVERT: G 17 MET cc_start: 0.4697 (ttt) cc_final: 0.4226 (tpt) REVERT: G 61 GLU cc_start: 0.7930 (mp0) cc_final: 0.7587 (mp0) REVERT: I 85 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: J 19 ARG cc_start: 0.8963 (mpt-90) cc_final: 0.8629 (mpp80) REVERT: J 58 ARG cc_start: 0.6899 (mmp-170) cc_final: 0.6632 (mmp80) REVERT: J 62 MET cc_start: 0.6352 (tpp) cc_final: 0.5711 (tpp) REVERT: J 102 LEU cc_start: 0.8893 (mp) cc_final: 0.8140 (tt) REVERT: K 17 MET cc_start: 0.3985 (tpp) cc_final: 0.1596 (pmm) REVERT: K 37 LEU cc_start: 0.9195 (tp) cc_final: 0.8849 (mm) REVERT: K 41 ARG cc_start: 0.8868 (mtp85) cc_final: 0.8522 (ptm-80) REVERT: L 26 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7114 (mt-10) REVERT: L 152 LEU cc_start: 0.8340 (mp) cc_final: 0.7835 (mt) REVERT: L 154 GLU cc_start: 0.6092 (pm20) cc_final: 0.5307 (tt0) REVERT: M 45 GLU cc_start: 0.7927 (tp30) cc_final: 0.7707 (tt0) REVERT: M 73 TYR cc_start: 0.8099 (m-80) cc_final: 0.7696 (m-80) REVERT: N 79 ASP cc_start: 0.9258 (t0) cc_final: 0.8969 (t0) REVERT: N 150 MET cc_start: 0.8517 (pmm) cc_final: 0.8129 (pmm) REVERT: O 92 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.6835 (t70) REVERT: R 58 ARG cc_start: 0.7750 (mmp-170) cc_final: 0.7237 (mmp80) REVERT: R 72 LYS cc_start: 0.8548 (ptmt) cc_final: 0.8233 (pttp) REVERT: T 18 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7441 (mt-10) REVERT: T 69 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6883 (t0) REVERT: T 169 GLU cc_start: 0.8658 (mp0) cc_final: 0.8229 (mp0) REVERT: V 19 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7603 (mpp80) REVERT: V 53 PRO cc_start: 0.6599 (Cg_endo) cc_final: 0.6236 (Cg_exo) REVERT: V 58 ARG cc_start: 0.7164 (mmp80) cc_final: 0.6260 (ptp90) REVERT: V 96 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8101 (pt0) REVERT: V 159 ARG cc_start: 0.7417 (tpp80) cc_final: 0.7084 (tpp80) REVERT: W 69 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.8169 (ttm-80) REVERT: W 78 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.7934 (t0) outliers start: 122 outliers final: 103 residues processed: 513 average time/residue: 0.3332 time to fit residues: 263.1390 Evaluate side-chains 519 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 411 time to evaluate : 2.575 ------------------------------------------------------------------------------- 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 98 ILE Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 27 LEU 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 170 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 C residue 97 ILE Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 38 ASP 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 144 ASN Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 39 GLU 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 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 126 VAL 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 G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 71 THR 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 L residue 165 ILE 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 M residue 86 ILE Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 122 ILE 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 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 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 142 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain S residue 17 MET 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 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 127 SER Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 47 ILE 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 156 ILE Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain W residue 78 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 84 optimal weight: 40.0000 chunk 172 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 239 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 185 optimal weight: 0.0670 chunk 263 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 271 optimal weight: 9.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN 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 = 0.4042 r_free = 0.4042 target = 0.123288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.100143 restraints weight = 79836.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.103094 restraints weight = 52835.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.105247 restraints weight = 39188.622| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.8520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22444 Z= 0.135 Angle : 0.749 10.667 30566 Z= 0.366 Chirality : 0.049 0.348 3753 Planarity : 0.006 0.059 3918 Dihedral : 5.137 55.524 3088 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.09 % Allowed : 33.48 % Favored : 62.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2862 helix: 1.36 (0.16), residues: 1035 sheet: -0.21 (0.19), residues: 717 loop : -1.04 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 112 HIS 0.006 0.001 HIS T 155 PHE 0.034 0.003 PHE M 115 TYR 0.019 0.001 TYR A 109 ARG 0.016 0.001 ARG T 179 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 1096) hydrogen bonds : angle 4.44688 ( 3153) covalent geometry : bond 0.00322 (22444) covalent geometry : angle 0.74866 (30566) ********************** 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 544 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 448 time to evaluate : 2.567 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: A 109 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7561 (t80) REVERT: B 116 ASP cc_start: 0.8234 (t0) cc_final: 0.7717 (p0) REVERT: C 21 GLU cc_start: 0.8509 (tp30) cc_final: 0.8201 (tp30) REVERT: C 54 LYS cc_start: 0.9109 (ttpp) cc_final: 0.8674 (ttpp) REVERT: D 24 ILE cc_start: 0.9050 (mp) cc_final: 0.8515 (tt) REVERT: D 69 ASP cc_start: 0.8027 (m-30) cc_final: 0.7720 (m-30) REVERT: D 112 GLU cc_start: 0.3768 (pm20) cc_final: 0.3396 (pm20) REVERT: D 115 LYS cc_start: 0.8612 (tmtt) cc_final: 0.7887 (mmtt) REVERT: E 31 LYS cc_start: 0.8484 (mttt) cc_final: 0.8274 (mmmt) REVERT: E 36 LYS cc_start: 0.8907 (mmtm) cc_final: 0.8116 (tptp) REVERT: E 115 PHE cc_start: 0.7580 (t80) cc_final: 0.7352 (t80) REVERT: F 90 ASP cc_start: 0.7861 (m-30) cc_final: 0.7564 (m-30) REVERT: F 159 ARG cc_start: 0.7939 (tpp80) cc_final: 0.7688 (tpp80) REVERT: G 17 MET cc_start: 0.4516 (ttt) cc_final: 0.4200 (tpt) REVERT: G 61 GLU cc_start: 0.7862 (mp0) cc_final: 0.7604 (mp0) REVERT: I 85 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6313 (m-80) REVERT: J 19 ARG cc_start: 0.8975 (mpt-90) cc_final: 0.8636 (mpp80) REVERT: J 32 ARG cc_start: 0.8505 (mtt-85) cc_final: 0.7596 (ttp-170) REVERT: J 62 MET cc_start: 0.6268 (tpp) cc_final: 0.5753 (tpp) REVERT: J 102 LEU cc_start: 0.8887 (mp) cc_final: 0.8186 (tt) REVERT: J 137 ASP cc_start: 0.8952 (t0) cc_final: 0.8738 (t0) REVERT: K 17 MET cc_start: 0.3664 (tpp) cc_final: 0.1686 (pmm) REVERT: K 37 LEU cc_start: 0.9222 (tp) cc_final: 0.8881 (mm) REVERT: K 41 ARG cc_start: 0.8865 (mtp85) cc_final: 0.8614 (ptm-80) REVERT: L 26 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7055 (mt-10) REVERT: M 17 MET cc_start: 0.1286 (OUTLIER) cc_final: 0.0975 (ptm) REVERT: M 73 TYR cc_start: 0.8088 (m-80) cc_final: 0.7589 (m-80) REVERT: N 79 ASP cc_start: 0.9211 (t0) cc_final: 0.8938 (t0) REVERT: N 150 MET cc_start: 0.8553 (pmm) cc_final: 0.8128 (pmm) REVERT: O 92 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6886 (t70) REVERT: R 58 ARG cc_start: 0.7721 (mmp-170) cc_final: 0.7187 (mmp80) REVERT: R 72 LYS cc_start: 0.8446 (ptmt) cc_final: 0.8158 (pttp) REVERT: S 17 MET cc_start: 0.3920 (OUTLIER) cc_final: 0.3437 (tpt) REVERT: T 18 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7539 (mt-10) REVERT: T 69 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6857 (t0) REVERT: T 169 GLU cc_start: 0.8649 (mp0) cc_final: 0.8241 (mp0) REVERT: V 19 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7756 (mpp80) REVERT: V 53 PRO cc_start: 0.6515 (Cg_endo) cc_final: 0.6150 (Cg_exo) REVERT: V 58 ARG cc_start: 0.7101 (mmp80) cc_final: 0.6180 (ptp90) REVERT: V 68 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8986 (mm-30) REVERT: V 69 ASP cc_start: 0.7861 (t0) cc_final: 0.7589 (t0) REVERT: V 96 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8045 (pt0) REVERT: V 159 ARG cc_start: 0.7362 (tpp80) cc_final: 0.7088 (tpp80) REVERT: W 17 MET cc_start: 0.5025 (mtm) cc_final: 0.4746 (mtt) REVERT: W 69 ARG cc_start: 0.8515 (ttm-80) cc_final: 0.8313 (ttm-80) REVERT: W 78 ASN cc_start: 0.8672 (m-40) cc_final: 0.7991 (t0) outliers start: 96 outliers final: 76 residues processed: 518 average time/residue: 0.3306 time to fit residues: 262.4680 Evaluate side-chains 503 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 420 time to evaluate : 2.507 ------------------------------------------------------------------------------- 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 98 ILE Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 170 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 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 144 ASN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 39 GLU 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 109 TYR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 64 LEU 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 126 VAL 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 G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 109 TYR Chi-restraints excluded: chain L residue 121 ILE 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 42 LEU Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 122 ILE 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 92 ASP Chi-restraints excluded: chain O residue 109 TYR 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 49 THR Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 137 ASP 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 S residue 17 MET Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 109 TYR 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 127 SER Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain U residue 24 THR 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 156 ILE Chi-restraints excluded: chain V residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 74 optimal weight: 0.0270 chunk 238 optimal weight: 8.9990 chunk 254 optimal weight: 7.9990 chunk 260 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 279 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 270 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 overall best weight: 2.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.121911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.099099 restraints weight = 80758.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.101957 restraints weight = 53594.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.104091 restraints weight = 39760.187| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.8689 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= 0.147 Angle : 0.761 13.202 30566 Z= 0.373 Chirality : 0.049 0.333 3753 Planarity : 0.006 0.066 3918 Dihedral : 5.170 56.232 3088 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.47 % Allowed : 33.22 % Favored : 62.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.16), residues: 2862 helix: 1.33 (0.16), residues: 1035 sheet: -0.18 (0.19), residues: 717 loop : -1.10 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 112 HIS 0.014 0.001 HIS I 90 PHE 0.030 0.003 PHE O 115 TYR 0.022 0.001 TYR A 109 ARG 0.015 0.001 ARG T 179 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 1096) hydrogen bonds : angle 4.49729 ( 3153) covalent geometry : bond 0.00351 (22444) covalent geometry : angle 0.76130 (30566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8488.55 seconds wall clock time: 148 minutes 34.02 seconds (8914.02 seconds total)