Starting phenix.real_space_refine on Wed Jun 18 21:23:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8un1_42390/06_2025/8un1_42390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8un1_42390/06_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_42390/06_2025/8un1_42390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8un1_42390/06_2025/8un1_42390.map" model { file = "/net/cci-nas-00/data/ceres_data/8un1_42390/06_2025/8un1_42390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8un1_42390/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.85, per 1000 atoms: 0.58 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: 4.98 Conformation dependent library (CDL) restraints added in 2.8 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: 2.35 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: 7.15 Time building geometry restraints manager: 5.99 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 48.030 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.120 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.940 ------------------------------------------------------------------------------- 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 : 4.887 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: 0.4680 time to fit residues: 678.9009 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 : 2.342 ------------------------------------------------------------------------------- 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 = 0.131911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.108654 restraints weight = 80194.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.111698 restraints weight = 53497.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.113929 restraints weight = 39731.033| |-----------------------------------------------------------------------------| 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 9.837 30566 Z= 0.445 Chirality : 0.054 0.323 3753 Planarity : 0.007 0.077 3918 Dihedral : 6.078 58.816 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 5.19618 ( 3153) covalent geometry : bond 0.00512 (22444) covalent geometry : angle 0.88690 (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 : 2.588 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: 0.5427 (mm) cc_final: 0.4967 (mm) REVERT: B 24 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6497 (tp) REVERT: B 69 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7089 (t0) REVERT: B 199 LEU cc_start: 0.9249 (pp) cc_final: 0.8927 (tp) REVERT: C 54 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8390 (ttpp) REVERT: C 55 ILE cc_start: 0.9188 (mm) cc_final: 0.8862 (tp) REVERT: D 24 ILE cc_start: 0.8902 (mp) cc_final: 0.8393 (tt) REVERT: D 52 GLU cc_start: 0.5097 (OUTLIER) cc_final: 0.4660 (pm20) REVERT: D 60 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8055 (tp) REVERT: D 90 ASP cc_start: 0.7807 (t0) cc_final: 0.7525 (t0) REVERT: E 36 LYS cc_start: 0.8597 (mmtm) cc_final: 0.8341 (tptp) REVERT: E 76 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8157 (mm-30) REVERT: E 77 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7576 (tm-30) REVERT: F 69 ASP cc_start: 0.6677 (OUTLIER) cc_final: 0.6328 (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: 0.7708 (tp30) cc_final: 0.7185 (tp30) REVERT: I 42 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6859 (tp) REVERT: I 92 ASP cc_start: 0.7904 (m-30) cc_final: 0.6958 (t70) REVERT: J 24 ILE cc_start: 0.5765 (OUTLIER) cc_final: 0.5211 (mp) REVERT: J 168 LYS cc_start: 0.8377 (mppt) cc_final: 0.8076 (mmmt) REVERT: K 77 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8374 (tp30) REVERT: L 69 ASP cc_start: 0.6779 (OUTLIER) cc_final: 0.6074 (t70) REVERT: M 33 ILE cc_start: 0.8988 (mt) cc_final: 0.8772 (mm) REVERT: Q 21 GLU cc_start: 0.5958 (tp30) cc_final: 0.5212 (mp0) REVERT: Q 98 ILE cc_start: 0.8279 (mp) cc_final: 0.8072 (mp) REVERT: R 58 ARG cc_start: 0.7714 (mmp-170) cc_final: 0.7265 (mmp80) REVERT: R 69 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7757 (t70) REVERT: S 40 ASN cc_start: 0.8562 (p0) cc_final: 0.8150 (p0) REVERT: T 62 MET cc_start: 0.7513 (tpp) cc_final: 0.6917 (tpp) REVERT: T 69 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.6318 (t0) REVERT: T 176 ARG cc_start: 0.7628 (ptt90) cc_final: 0.7403 (ttm110) REVERT: V 19 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7399 (mpt-90) REVERT: V 53 PRO cc_start: 0.5534 (Cg_endo) cc_final: 0.5206 (Cg_exo) REVERT: V 60 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6565 (tp) REVERT: V 74 MET cc_start: 0.9347 (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: 0.7930 (pp) cc_final: 0.7373 (tp) REVERT: W 42 LEU cc_start: 0.7354 (tp) cc_final: 0.6893 (tt) REVERT: W 78 ASN cc_start: 0.8342 (t0) cc_final: 0.7628 (t0) REVERT: W 86 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8886 (pt) outliers start: 183 outliers final: 89 residues processed: 691 average time/residue: 0.3382 time to fit residues: 356.7466 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 : 2.667 ------------------------------------------------------------------------------- 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: 10.0000 chunk 265 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.124692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.101920 restraints weight = 81275.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.104813 restraints weight = 54148.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.106905 restraints weight = 40278.394| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5854 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= 0.223 Angle : 0.837 12.445 30566 Z= 0.422 Chirality : 0.052 0.276 3753 Planarity : 0.007 0.103 3918 Dihedral : 6.023 58.261 3092 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 8.65 % Allowed : 25.98 % Favored : 65.37 % 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: -0.50 (0.16), residues: 2862 helix: 0.66 (0.15), residues: 1023 sheet: -0.88 (0.16), residues: 912 loop : -0.60 (0.22), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 112 HIS 0.041 0.002 HIS V 155 PHE 0.032 0.003 PHE E 115 TYR 0.032 0.002 TYR A 109 ARG 0.007 0.001 ARG R 141 Details of bonding type rmsd hydrogen bonds : bond 0.05477 ( 1096) hydrogen bonds : angle 5.15409 ( 3153) covalent geometry : bond 0.00511 (22444) covalent geometry : angle 0.83705 (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 679 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 476 time to evaluate : 2.872 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: A 94 ILE cc_start: 0.5471 (mm) cc_final: 0.4971 (mm) REVERT: A 109 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.7171 (t80) REVERT: B 69 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7224 (t0) REVERT: B 199 LEU cc_start: 0.9327 (pp) cc_final: 0.8969 (tp) REVERT: C 49 THR cc_start: 0.8329 (t) cc_final: 0.7940 (p) REVERT: C 54 LYS cc_start: 0.8986 (ttpp) cc_final: 0.8584 (ttpp) REVERT: D 24 ILE cc_start: 0.9192 (mp) cc_final: 0.8522 (tt) REVERT: D 30 TYR cc_start: 0.8157 (t80) cc_final: 0.7931 (t80) REVERT: D 68 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8216 (tp30) REVERT: D 69 ASP cc_start: 0.7215 (m-30) cc_final: 0.6972 (m-30) REVERT: D 90 ASP cc_start: 0.7879 (t0) cc_final: 0.7636 (t0) REVERT: E 36 LYS cc_start: 0.8524 (mmtm) cc_final: 0.7755 (tptp) REVERT: E 77 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7544 (tm-30) REVERT: E 115 PHE cc_start: 0.7660 (t80) cc_final: 0.6438 (t80) REVERT: F 19 ARG cc_start: 0.7201 (mtp85) cc_final: 0.6944 (mtt-85) REVERT: F 69 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6820 (t0) REVERT: F 90 ASP cc_start: 0.7742 (m-30) cc_final: 0.7375 (m-30) REVERT: F 142 LEU cc_start: 0.8641 (tt) cc_final: 0.8434 (tt) REVERT: G 36 LYS cc_start: 0.9340 (mmtm) cc_final: 0.8859 (tptp) REVERT: G 75 GLU cc_start: 0.6894 (pm20) cc_final: 0.5702 (pm20) REVERT: I 35 LYS cc_start: 0.9017 (tptp) cc_final: 0.8778 (tptp) REVERT: I 78 ASN cc_start: 0.5070 (OUTLIER) cc_final: 0.4864 (m-40) REVERT: J 62 MET cc_start: 0.6396 (tpp) cc_final: 0.5866 (tpp) REVERT: J 142 LEU cc_start: 0.6863 (tp) cc_final: 0.5396 (tp) REVERT: K 41 ARG cc_start: 0.8836 (mtp85) cc_final: 0.8631 (mtp85) REVERT: L 128 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8346 (p) REVERT: L 179 ARG cc_start: 0.9120 (ttm110) cc_final: 0.8901 (ttm110) REVERT: M 33 ILE cc_start: 0.9127 (mt) cc_final: 0.8916 (mm) REVERT: M 52 LEU cc_start: 0.6566 (mm) cc_final: 0.6024 (mp) REVERT: M 69 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8170 (ptm160) REVERT: O 17 MET cc_start: 0.5654 (mmm) cc_final: 0.5451 (mmm) REVERT: O 28 GLU cc_start: 0.8631 (pm20) cc_final: 0.8313 (pm20) REVERT: Q 112 TRP cc_start: 0.7850 (t-100) cc_final: 0.7271 (t-100) REVERT: Q 116 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7578 (tp30) REVERT: R 58 ARG cc_start: 0.7697 (mmp-170) cc_final: 0.7355 (mmp80) REVERT: R 69 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7782 (t70) REVERT: R 90 ASP cc_start: 0.8182 (t0) cc_final: 0.7971 (t0) REVERT: S 21 GLU cc_start: 0.8716 (tp30) cc_final: 0.8201 (tp30) REVERT: T 69 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6606 (t0) REVERT: V 19 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7455 (mpp80) REVERT: V 53 PRO cc_start: 0.5762 (Cg_endo) cc_final: 0.5358 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6466 (mmp80) cc_final: 0.5654 (mtt180) REVERT: V 96 GLU cc_start: 0.8599 (mm-30) cc_final: 0.7800 (pt0) REVERT: V 112 GLU cc_start: 0.7928 (mp0) cc_final: 0.7423 (pp20) REVERT: V 168 LYS cc_start: 0.9453 (tttt) cc_final: 0.9153 (tppt) REVERT: V 172 GLU cc_start: 0.9445 (OUTLIER) cc_final: 0.9133 (mm-30) REVERT: W 42 LEU cc_start: 0.7610 (tp) cc_final: 0.7148 (tt) REVERT: W 78 ASN cc_start: 0.8399 (t0) cc_final: 0.7820 (t0) REVERT: W 86 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8831 (pt) outliers start: 203 outliers final: 123 residues processed: 606 average time/residue: 0.3662 time to fit residues: 339.6536 Evaluate side-chains 550 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 417 time to evaluate : 2.371 ------------------------------------------------------------------------------- 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 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 48 ILE Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 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 80 VAL 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 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 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 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 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 71 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 99 VAL 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 128 THR Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 148 THR 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 M residue 69 ARG 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 20 ILE 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 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 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 S residue 77 GLU Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 46 VAL 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 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 86 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 152 LEU Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 172 GLU 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 Chi-restraints excluded: chain W residue 92 ASP Chi-restraints excluded: chain W residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 129 optimal weight: 1.9990 chunk 253 optimal weight: 0.0870 chunk 223 optimal weight: 0.2980 chunk 224 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.127718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.104507 restraints weight = 79973.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.107567 restraints weight = 52803.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.109791 restraints weight = 38925.475| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.6260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22444 Z= 0.139 Angle : 0.736 11.229 30566 Z= 0.364 Chirality : 0.050 0.245 3753 Planarity : 0.006 0.061 3918 Dihedral : 5.575 54.529 3090 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.37 % Allowed : 29.39 % Favored : 65.25 % 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: -0.10 (0.16), residues: 2862 helix: 1.04 (0.16), residues: 1032 sheet: -0.64 (0.17), residues: 888 loop : -0.52 (0.22), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 112 HIS 0.009 0.001 HIS V 155 PHE 0.034 0.003 PHE Q 115 TYR 0.022 0.002 TYR E 109 ARG 0.008 0.001 ARG J 141 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 1096) hydrogen bonds : angle 4.64461 ( 3153) covalent geometry : bond 0.00319 (22444) covalent geometry : angle 0.73570 (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 600 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 474 time to evaluate : 2.351 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: A 94 ILE cc_start: 0.5238 (mm) cc_final: 0.4724 (mm) REVERT: A 109 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.7097 (t80) REVERT: B 199 LEU cc_start: 0.9332 (pp) cc_final: 0.8986 (tp) REVERT: C 54 LYS cc_start: 0.9079 (ttpp) cc_final: 0.8693 (ttpp) REVERT: D 24 ILE cc_start: 0.9018 (mp) cc_final: 0.8428 (tt) REVERT: D 52 GLU cc_start: 0.4920 (OUTLIER) cc_final: 0.4661 (pm20) REVERT: D 68 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8308 (tp30) REVERT: E 31 LYS cc_start: 0.8546 (mttt) cc_final: 0.8209 (mmmt) REVERT: E 36 LYS cc_start: 0.8462 (mmtm) cc_final: 0.7666 (tptp) REVERT: E 75 GLU cc_start: 0.8195 (pm20) cc_final: 0.7738 (pm20) REVERT: E 76 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7950 (mm-30) REVERT: E 77 GLU cc_start: 0.7796 (tm-30) cc_final: 0.6990 (tm-30) REVERT: E 78 ASN cc_start: 0.8120 (m-40) cc_final: 0.7876 (m-40) REVERT: E 115 PHE cc_start: 0.7149 (t80) cc_final: 0.6879 (t80) REVERT: F 19 ARG cc_start: 0.7239 (mtp85) cc_final: 0.6943 (mtt-85) REVERT: F 69 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6593 (t70) REVERT: F 90 ASP cc_start: 0.7826 (m-30) cc_final: 0.7566 (m-30) REVERT: G 36 LYS cc_start: 0.9311 (mmtm) cc_final: 0.8948 (tptp) REVERT: G 77 GLU cc_start: 0.8764 (mp0) cc_final: 0.8246 (pp20) REVERT: J 19 ARG cc_start: 0.8704 (mmt180) cc_final: 0.8253 (mpp80) REVERT: J 62 MET cc_start: 0.6260 (tpp) cc_final: 0.5684 (tpp) REVERT: K 17 MET cc_start: 0.3697 (mmm) cc_final: 0.1013 (pmm) REVERT: K 41 ARG cc_start: 0.8813 (mtp85) cc_final: 0.8139 (tpp-160) REVERT: M 52 LEU cc_start: 0.6768 (mm) cc_final: 0.6492 (mp) REVERT: N 61 ILE cc_start: 0.8729 (tt) cc_final: 0.8480 (mp) REVERT: O 28 GLU cc_start: 0.8637 (pm20) cc_final: 0.8388 (pm20) REVERT: R 58 ARG cc_start: 0.7768 (mmp-170) cc_final: 0.7507 (mmp80) REVERT: R 142 LEU cc_start: 0.6358 (tp) cc_final: 0.6148 (tp) REVERT: S 17 MET cc_start: 0.2295 (ptm) cc_final: 0.1821 (mpp) REVERT: S 21 GLU cc_start: 0.8727 (tp30) cc_final: 0.8167 (tp30) REVERT: S 40 ASN cc_start: 0.8324 (p0) cc_final: 0.8056 (p0) REVERT: S 42 LEU cc_start: 0.8583 (mt) cc_final: 0.8259 (mt) REVERT: T 69 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6622 (t0) REVERT: U 54 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8546 (mmmt) REVERT: U 115 PHE cc_start: 0.6092 (t80) cc_final: 0.5890 (t80) REVERT: V 19 ARG cc_start: 0.7634 (mtm-85) cc_final: 0.7225 (mpp80) REVERT: V 53 PRO cc_start: 0.5857 (Cg_endo) cc_final: 0.5447 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6421 (mmp80) cc_final: 0.5526 (ptp-170) REVERT: V 74 MET cc_start: 0.9282 (mmm) cc_final: 0.9053 (mmm) REVERT: V 96 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7745 (pt0) REVERT: W 42 LEU cc_start: 0.7561 (tp) cc_final: 0.7257 (pp) REVERT: W 78 ASN cc_start: 0.8429 (m-40) cc_final: 0.7906 (t0) outliers start: 126 outliers final: 71 residues processed: 554 average time/residue: 0.3263 time to fit residues: 274.5734 Evaluate side-chains 502 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 427 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET 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 61 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 24 THR Chi-restraints excluded: chain C residue 64 SER 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 140 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 189 LEU 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 J residue 79 ASP Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 168 LYS Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 178 ILE 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 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 71 THR 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 U residue 22 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain W residue 31 LYS Chi-restraints excluded: chain W residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 95 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 K 78 ASN ** N 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 GLN R 155 HIS 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.121569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.098606 restraints weight = 80340.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.101413 restraints weight = 53450.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.103506 restraints weight = 39809.535| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.7026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 22444 Z= 0.210 Angle : 0.777 11.844 30566 Z= 0.393 Chirality : 0.051 0.396 3753 Planarity : 0.006 0.054 3918 Dihedral : 5.622 53.979 3088 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 7.11 % Allowed : 28.49 % Favored : 64.40 % 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: -0.20 (0.16), residues: 2862 helix: 1.00 (0.16), residues: 1023 sheet: -0.72 (0.17), residues: 804 loop : -0.61 (0.21), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 112 HIS 0.021 0.002 HIS V 155 PHE 0.038 0.003 PHE E 115 TYR 0.030 0.002 TYR A 109 ARG 0.013 0.001 ARG N 141 Details of bonding type rmsd hydrogen bonds : bond 0.04889 ( 1096) hydrogen bonds : angle 4.89837 ( 3153) covalent geometry : bond 0.00492 (22444) covalent geometry : angle 0.77749 (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 606 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 439 time to evaluate : 2.350 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 58 GLU cc_start: 0.7308 (tt0) cc_final: 0.6813 (tm-30) REVERT: A 109 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.7333 (t80) REVERT: B 199 LEU cc_start: 0.9398 (pp) cc_final: 0.8966 (tp) REVERT: C 54 LYS cc_start: 0.9104 (ttpp) cc_final: 0.8729 (ttpp) REVERT: D 24 ILE cc_start: 0.9163 (mp) cc_final: 0.8490 (tt) REVERT: D 68 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8113 (tp30) REVERT: E 31 LYS cc_start: 0.8574 (mttt) cc_final: 0.8260 (mmmt) REVERT: E 36 LYS cc_start: 0.8708 (mmtm) cc_final: 0.8008 (tptp) REVERT: E 77 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7546 (tm-30) REVERT: F 69 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7198 (t0) REVERT: F 90 ASP cc_start: 0.7920 (m-30) cc_final: 0.7591 (m-30) REVERT: G 36 LYS cc_start: 0.9301 (mmtm) cc_final: 0.8865 (tptp) REVERT: G 77 GLU cc_start: 0.8634 (mp0) cc_final: 0.8430 (pm20) REVERT: I 35 LYS cc_start: 0.8997 (tptp) cc_final: 0.8762 (tptp) REVERT: J 19 ARG cc_start: 0.8964 (mmt180) cc_final: 0.8445 (pmt-80) REVERT: J 32 ARG cc_start: 0.8522 (mtt-85) cc_final: 0.8176 (ttm-80) REVERT: J 62 MET cc_start: 0.6352 (tpp) cc_final: 0.5750 (tpp) REVERT: K 41 ARG cc_start: 0.8888 (mtp85) cc_final: 0.8282 (tpp-160) REVERT: L 26 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6859 (mt-10) REVERT: M 52 LEU cc_start: 0.7049 (mm) cc_final: 0.6781 (mp) REVERT: R 58 ARG cc_start: 0.7734 (mmp-170) cc_final: 0.7322 (mmp80) REVERT: S 17 MET cc_start: 0.2749 (ptm) cc_final: 0.2187 (mpp) REVERT: S 21 GLU cc_start: 0.8666 (tp30) cc_final: 0.8185 (tp30) REVERT: S 42 LEU cc_start: 0.8633 (mt) cc_final: 0.8259 (mt) REVERT: T 69 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6742 (t0) REVERT: V 19 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7317 (mpp80) REVERT: V 53 PRO cc_start: 0.6012 (Cg_endo) cc_final: 0.5640 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6649 (mmp80) cc_final: 0.5820 (ptp-170) REVERT: V 96 GLU cc_start: 0.8656 (mm-30) cc_final: 0.7990 (pt0) REVERT: W 78 ASN cc_start: 0.8650 (m-40) cc_final: 0.8226 (t0) outliers start: 167 outliers final: 110 residues processed: 549 average time/residue: 0.3449 time to fit residues: 289.0720 Evaluate side-chains 507 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 394 time to evaluate : 2.567 ------------------------------------------------------------------------------- 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 54 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 138 VAL 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 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 24 ILE 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 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 86 ILE Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 48 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 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 52 GLU Chi-restraints excluded: chain L residue 93 LEU 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 M residue 17 MET Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain R residue 35 LYS Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 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 47 ILE Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 152 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 79 optimal weight: 6.9990 chunk 205 optimal weight: 20.0000 chunk 221 optimal weight: 7.9990 chunk 280 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.122975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.100095 restraints weight = 79954.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.102978 restraints weight = 53254.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.105063 restraints weight = 39659.709| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.7406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 22444 Z= 0.159 Angle : 0.736 11.643 30566 Z= 0.366 Chirality : 0.049 0.257 3753 Planarity : 0.006 0.057 3918 Dihedral : 5.514 54.503 3088 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 6.30 % Allowed : 29.56 % Favored : 64.14 % 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: -0.11 (0.16), residues: 2862 helix: 1.15 (0.16), residues: 1023 sheet: -0.60 (0.18), residues: 747 loop : -0.75 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 112 HIS 0.005 0.001 HIS T 155 PHE 0.021 0.003 PHE O 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 0.04345 ( 1096) hydrogen bonds : angle 4.67653 ( 3153) covalent geometry : bond 0.00384 (22444) covalent geometry : angle 0.73557 (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 581 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 433 time to evaluate : 2.446 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 58 GLU cc_start: 0.7431 (tt0) cc_final: 0.6911 (tm-30) REVERT: A 109 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.7236 (t80) REVERT: A 116 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8270 (mm-30) REVERT: B 199 LEU cc_start: 0.9440 (pp) cc_final: 0.9011 (tp) REVERT: C 54 LYS cc_start: 0.9104 (ttpp) cc_final: 0.8673 (ttpp) REVERT: D 24 ILE cc_start: 0.9128 (mp) cc_final: 0.8469 (tt) REVERT: D 68 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8415 (tp30) REVERT: E 31 LYS cc_start: 0.8547 (mttt) cc_final: 0.8292 (mmmt) REVERT: E 36 LYS cc_start: 0.8686 (mmtm) cc_final: 0.7949 (tptp) REVERT: F 90 ASP cc_start: 0.7864 (m-30) cc_final: 0.7576 (m-30) REVERT: F 159 ARG cc_start: 0.7970 (tpp80) cc_final: 0.7690 (tpp80) REVERT: G 17 MET cc_start: 0.4272 (ttt) cc_final: 0.3818 (tpt) REVERT: G 36 LYS cc_start: 0.9283 (mmtm) cc_final: 0.8867 (tptp) REVERT: G 77 GLU cc_start: 0.8618 (mp0) cc_final: 0.8347 (pp20) REVERT: I 35 LYS cc_start: 0.9064 (tptp) cc_final: 0.8793 (tptp) REVERT: I 85 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6503 (m-80) REVERT: J 19 ARG cc_start: 0.9016 (mmt180) cc_final: 0.8443 (pmt-80) REVERT: J 32 ARG cc_start: 0.8520 (mtt-85) cc_final: 0.8104 (ttm-80) REVERT: J 62 MET cc_start: 0.6286 (tpp) cc_final: 0.5550 (tpp) REVERT: K 17 MET cc_start: 0.3885 (tpp) cc_final: 0.0775 (pmm) REVERT: K 37 LEU cc_start: 0.9022 (tp) cc_final: 0.8726 (mm) REVERT: K 41 ARG cc_start: 0.8964 (mtp85) cc_final: 0.8447 (ptm-80) REVERT: L 26 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6863 (mt-10) REVERT: N 137 ASP cc_start: 0.8942 (t0) cc_final: 0.8430 (t0) REVERT: O 28 GLU cc_start: 0.8838 (pm20) cc_final: 0.8479 (pm20) REVERT: R 58 ARG cc_start: 0.7694 (mmp-170) cc_final: 0.7273 (mmp80) REVERT: S 17 MET cc_start: 0.3136 (OUTLIER) cc_final: 0.2636 (mpp) REVERT: S 42 LEU cc_start: 0.8763 (mt) cc_final: 0.8381 (mt) REVERT: T 18 GLU cc_start: 0.7875 (mm-30) cc_final: 0.6989 (mt-10) REVERT: T 69 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6792 (t0) REVERT: V 19 ARG cc_start: 0.8028 (mtm-85) cc_final: 0.7490 (mpp80) REVERT: V 53 PRO cc_start: 0.6015 (Cg_endo) cc_final: 0.5629 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6714 (mmp80) cc_final: 0.5899 (ptp-170) REVERT: V 96 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7974 (pt0) REVERT: W 17 MET cc_start: 0.5318 (OUTLIER) cc_final: 0.5085 (mtm) REVERT: W 78 ASN cc_start: 0.8709 (m-40) cc_final: 0.8196 (t0) outliers start: 148 outliers final: 104 residues processed: 529 average time/residue: 0.3360 time to fit residues: 270.3351 Evaluate side-chains 502 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 393 time to evaluate : 2.362 ------------------------------------------------------------------------------- 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 C residue 24 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 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 33 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 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 86 ILE Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 48 ILE 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 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 129 VAL 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 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 189 LEU Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 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 61 ILE Chi-restraints excluded: chain R residue 80 VAL 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 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 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 122 ILE 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 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 129 VAL Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 156 ILE 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 31 LYS Chi-restraints excluded: chain W residue 71 THR 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: 0.9990 chunk 170 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 222 optimal weight: 0.4980 chunk 95 optimal weight: 20.0000 chunk 237 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 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 = 0.4052 r_free = 0.4052 target = 0.123766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.100939 restraints weight = 80780.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.104070 restraints weight = 52443.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.106313 restraints weight = 38322.448| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.7716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 22444 Z= 0.143 Angle : 0.731 10.739 30566 Z= 0.362 Chirality : 0.049 0.262 3753 Planarity : 0.006 0.054 3918 Dihedral : 5.362 55.458 3088 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.92 % Allowed : 30.11 % Favored : 63.97 % 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: 1.29 (0.16), residues: 1032 sheet: -0.51 (0.18), residues: 747 loop : -0.76 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 112 HIS 0.006 0.001 HIS T 155 PHE 0.024 0.003 PHE M 115 TYR 0.022 0.002 TYR A 109 ARG 0.011 0.001 ARG L 179 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 1096) hydrogen bonds : angle 4.53259 ( 3153) covalent geometry : bond 0.00340 (22444) covalent geometry : angle 0.73119 (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: 139 poor density : 438 time to evaluate : 2.369 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: A 58 GLU cc_start: 0.7405 (tt0) cc_final: 0.6888 (tm-30) REVERT: A 109 TYR cc_start: 0.7720 (OUTLIER) cc_final: 0.7217 (t80) REVERT: A 116 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8178 (mm-30) REVERT: B 62 MET cc_start: 0.8669 (tpp) cc_final: 0.8345 (mmm) REVERT: B 199 LEU cc_start: 0.9461 (pp) cc_final: 0.9058 (tp) REVERT: C 54 LYS cc_start: 0.9124 (ttpp) cc_final: 0.8698 (ttpp) REVERT: D 24 ILE cc_start: 0.9041 (mp) cc_final: 0.8422 (tt) REVERT: D 112 GLU cc_start: 0.3518 (pm20) cc_final: 0.3158 (pm20) REVERT: E 31 LYS cc_start: 0.8568 (mttt) cc_final: 0.8314 (mmmt) REVERT: E 36 LYS cc_start: 0.8771 (mmtm) cc_final: 0.7979 (tptp) REVERT: F 90 ASP cc_start: 0.7963 (m-30) cc_final: 0.7658 (m-30) REVERT: F 159 ARG cc_start: 0.8015 (tpp80) cc_final: 0.7751 (tpp80) REVERT: G 17 MET cc_start: 0.4451 (ttt) cc_final: 0.3823 (tpt) REVERT: I 85 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.6460 (m-80) REVERT: J 19 ARG cc_start: 0.9060 (mmt180) cc_final: 0.8474 (pmt-80) REVERT: J 32 ARG cc_start: 0.8573 (mtt-85) cc_final: 0.8114 (ttm-80) REVERT: J 58 ARG cc_start: 0.6892 (mmp-170) cc_final: 0.6539 (mmp80) REVERT: J 62 MET cc_start: 0.6263 (tpp) cc_final: 0.5553 (tpp) REVERT: J 102 LEU cc_start: 0.9268 (mt) cc_final: 0.9064 (mm) REVERT: K 17 MET cc_start: 0.3763 (tpp) cc_final: 0.0811 (pmm) REVERT: K 37 LEU cc_start: 0.9000 (tp) cc_final: 0.8688 (mm) REVERT: K 41 ARG cc_start: 0.8950 (mtp85) cc_final: 0.8548 (ptm-80) REVERT: L 26 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7188 (mt-10) REVERT: O 92 ASP cc_start: 0.7387 (m-30) cc_final: 0.6830 (t70) REVERT: R 42 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8634 (mmmt) REVERT: R 58 ARG cc_start: 0.7679 (mmp-170) cc_final: 0.7192 (mmp80) REVERT: R 72 LYS cc_start: 0.8529 (ptmt) cc_final: 0.8220 (pttp) REVERT: S 17 MET cc_start: 0.3425 (OUTLIER) cc_final: 0.3104 (mpp) REVERT: S 42 LEU cc_start: 0.8781 (mt) cc_final: 0.8375 (mt) REVERT: T 18 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7119 (mt-10) REVERT: T 69 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6785 (t0) REVERT: T 96 GLU cc_start: 0.8751 (mp0) cc_final: 0.8513 (mp0) REVERT: T 167 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8562 (t0) REVERT: T 169 GLU cc_start: 0.8551 (mp0) cc_final: 0.8164 (mp0) REVERT: V 19 ARG cc_start: 0.8041 (mtm-85) cc_final: 0.7551 (mpp80) REVERT: V 53 PRO cc_start: 0.6142 (Cg_endo) cc_final: 0.5770 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6872 (mmp80) cc_final: 0.6011 (ptp-170) REVERT: V 96 GLU cc_start: 0.8596 (mm-30) cc_final: 0.7980 (pt0) REVERT: W 78 ASN cc_start: 0.8667 (m-40) cc_final: 0.8147 (t0) outliers start: 139 outliers final: 96 residues processed: 530 average time/residue: 0.3500 time to fit residues: 281.3604 Evaluate side-chains 509 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 408 time to evaluate : 2.677 ------------------------------------------------------------------------------- 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 101 THR 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 152 LEU 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 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 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 24 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 46 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 109 TYR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 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 K residue 71 THR Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 121 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 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 189 LEU 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 99 VAL Chi-restraints excluded: chain Q residue 112 TRP 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 142 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 189 LEU 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 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 123 VAL Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 167 ASP Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 24 THR 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 54 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 142 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain W residue 31 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 260 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 252 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 277 optimal weight: 30.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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** ** 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** ** T 98 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 = 0.4020 r_free = 0.4020 target = 0.121911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.099114 restraints weight = 80889.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.102046 restraints weight = 53679.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.104173 restraints weight = 39738.300| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.8036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 22444 Z= 0.155 Angle : 0.753 10.385 30566 Z= 0.371 Chirality : 0.049 0.321 3753 Planarity : 0.006 0.052 3918 Dihedral : 5.334 56.189 3088 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.96 % Allowed : 30.62 % Favored : 63.42 % 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: 1.32 (0.16), residues: 1032 sheet: -0.35 (0.19), residues: 711 loop : -0.92 (0.20), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 112 HIS 0.005 0.001 HIS T 155 PHE 0.026 0.003 PHE M 115 TYR 0.025 0.002 TYR A 109 ARG 0.012 0.001 ARG L 179 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 1096) hydrogen bonds : angle 4.55991 ( 3153) covalent geometry : bond 0.00374 (22444) covalent geometry : angle 0.75321 (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 566 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 426 time to evaluate : 2.390 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: 0.7865 (OUTLIER) cc_final: 0.7342 (t80) REVERT: A 116 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8191 (mm-30) REVERT: B 60 LEU cc_start: 0.8877 (tp) cc_final: 0.8661 (tt) REVERT: B 116 ASP cc_start: 0.8186 (t0) cc_final: 0.7719 (p0) REVERT: B 199 LEU cc_start: 0.9455 (pp) cc_final: 0.9021 (tp) REVERT: C 54 LYS cc_start: 0.9098 (ttpp) cc_final: 0.8679 (ttpp) REVERT: D 24 ILE cc_start: 0.9029 (mp) cc_final: 0.8411 (tt) REVERT: E 31 LYS cc_start: 0.8581 (mttt) cc_final: 0.8348 (mmmt) REVERT: E 36 LYS cc_start: 0.8849 (mmtm) cc_final: 0.8089 (tptp) REVERT: F 90 ASP cc_start: 0.7913 (m-30) cc_final: 0.7614 (m-30) REVERT: F 159 ARG cc_start: 0.7999 (tpp80) cc_final: 0.7768 (tpp80) REVERT: G 17 MET cc_start: 0.4623 (ttt) cc_final: 0.4015 (tpt) REVERT: G 36 LYS cc_start: 0.9231 (mmtm) cc_final: 0.8824 (tptp) REVERT: I 85 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6502 (m-80) REVERT: J 19 ARG cc_start: 0.9165 (mmt180) cc_final: 0.8493 (pmt-80) REVERT: J 35 LYS cc_start: 0.9190 (tppp) cc_final: 0.8830 (tppt) REVERT: J 58 ARG cc_start: 0.6912 (mmp-170) cc_final: 0.6616 (mmp80) REVERT: J 62 MET cc_start: 0.6330 (tpp) cc_final: 0.5625 (tpp) REVERT: K 17 MET cc_start: 0.3832 (tpp) cc_final: 0.1076 (pmm) REVERT: K 37 LEU cc_start: 0.9018 (tp) cc_final: 0.8680 (mm) REVERT: K 41 ARG cc_start: 0.8907 (mtp85) cc_final: 0.8560 (ptm-80) REVERT: L 26 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6990 (mt-10) REVERT: L 74 MET cc_start: 0.9166 (mmp) cc_final: 0.8942 (mmt) REVERT: O 69 ARG cc_start: 0.8561 (tmm-80) cc_final: 0.8339 (tmm-80) REVERT: O 92 ASP cc_start: 0.7372 (m-30) cc_final: 0.6843 (t70) REVERT: R 42 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8741 (mmmt) REVERT: R 58 ARG cc_start: 0.7693 (mmp-170) cc_final: 0.7188 (mmp80) REVERT: S 17 MET cc_start: 0.3410 (OUTLIER) cc_final: 0.3201 (mpp) REVERT: S 42 LEU cc_start: 0.8856 (mt) cc_final: 0.8475 (mt) REVERT: T 18 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7218 (mt-10) REVERT: T 69 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.6818 (t0) REVERT: T 167 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8536 (t0) REVERT: T 169 GLU cc_start: 0.8527 (mp0) cc_final: 0.8104 (mp0) REVERT: V 19 ARG cc_start: 0.8101 (mtm-85) cc_final: 0.7614 (mpp80) REVERT: V 53 PRO cc_start: 0.6387 (Cg_endo) cc_final: 0.6036 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6959 (mmp80) cc_final: 0.6105 (ptp-170) REVERT: V 62 MET cc_start: 0.8122 (ttm) cc_final: 0.7882 (ttm) REVERT: V 96 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8009 (pt0) REVERT: W 78 ASN cc_start: 0.8659 (m-40) cc_final: 0.8093 (t0) outliers start: 140 outliers final: 107 residues processed: 517 average time/residue: 0.3322 time to fit residues: 263.2291 Evaluate side-chains 527 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 415 time to evaluate : 2.382 ------------------------------------------------------------------------------- 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 101 THR 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 48 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 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 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 33 ILE 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 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 79 VAL Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 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 K residue 74 THR Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 121 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 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 196 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 48 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain R residue 35 LYS 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 R residue 189 LEU 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 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 T residue 167 ASP Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 24 THR 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 54 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 142 LEU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain W residue 31 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 90 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 247 optimal weight: 9.9990 chunk 19 optimal weight: 0.0060 chunk 134 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- 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 202 ASN ** N 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** T 98 HIS V 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.120015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.097188 restraints weight = 80691.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.099988 restraints weight = 54173.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.102038 restraints weight = 40485.488| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.8442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 22444 Z= 0.172 Angle : 0.771 10.083 30566 Z= 0.382 Chirality : 0.050 0.268 3753 Planarity : 0.006 0.061 3918 Dihedral : 5.438 56.441 3088 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.71 % Allowed : 31.05 % 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: -0.15 (0.16), residues: 2862 helix: 1.21 (0.16), residues: 1035 sheet: -0.49 (0.18), residues: 756 loop : -1.01 (0.20), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 112 HIS 0.006 0.001 HIS R 155 PHE 0.029 0.003 PHE M 115 TYR 0.027 0.002 TYR A 109 ARG 0.017 0.001 ARG T 179 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 1096) hydrogen bonds : angle 4.67165 ( 3153) covalent geometry : bond 0.00406 (22444) covalent geometry : angle 0.77121 (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 562 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 428 time to evaluate : 2.360 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: A 109 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7482 (t80) REVERT: C 54 LYS cc_start: 0.9117 (ttpp) cc_final: 0.8733 (ttpp) REVERT: D 24 ILE cc_start: 0.9111 (mp) cc_final: 0.8461 (tt) REVERT: E 31 LYS cc_start: 0.8620 (mttt) cc_final: 0.8415 (mmmt) REVERT: E 36 LYS cc_start: 0.9000 (mmtm) cc_final: 0.8270 (tptp) REVERT: F 69 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7423 (t0) REVERT: F 90 ASP cc_start: 0.7876 (m-30) cc_final: 0.7573 (m-30) REVERT: F 159 ARG cc_start: 0.8040 (tpp80) cc_final: 0.7795 (tpp80) REVERT: G 17 MET cc_start: 0.4819 (ttt) cc_final: 0.4296 (tpt) REVERT: G 36 LYS cc_start: 0.9219 (mmtm) cc_final: 0.8943 (tptp) REVERT: J 19 ARG cc_start: 0.9230 (mmt180) cc_final: 0.8522 (ppt170) REVERT: J 35 LYS cc_start: 0.9164 (tppp) cc_final: 0.8789 (tppt) REVERT: J 58 ARG cc_start: 0.6908 (mmp-170) cc_final: 0.6649 (mmp80) REVERT: J 62 MET cc_start: 0.6277 (tpp) cc_final: 0.5443 (tpp) REVERT: J 102 LEU cc_start: 0.8837 (mp) cc_final: 0.8173 (tt) REVERT: K 17 MET cc_start: 0.4180 (tpp) cc_final: 0.1234 (pmm) REVERT: K 37 LEU cc_start: 0.9118 (tp) cc_final: 0.8738 (mm) REVERT: K 41 ARG cc_start: 0.8858 (mtp85) cc_final: 0.8596 (ptm-80) REVERT: L 26 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6914 (mt-10) REVERT: N 79 ASP cc_start: 0.9328 (t0) cc_final: 0.9008 (t0) REVERT: O 92 ASP cc_start: 0.7479 (m-30) cc_final: 0.6932 (t70) REVERT: R 58 ARG cc_start: 0.7689 (mmp-170) cc_final: 0.7152 (mmp80) REVERT: S 17 MET cc_start: 0.4085 (OUTLIER) cc_final: 0.3789 (mpp) REVERT: T 18 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7509 (mt-10) REVERT: T 69 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.6898 (t0) REVERT: T 167 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8567 (t0) REVERT: T 169 GLU cc_start: 0.8528 (mp0) cc_final: 0.8130 (mp0) REVERT: V 19 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7667 (mpp80) REVERT: V 53 PRO cc_start: 0.6549 (Cg_endo) cc_final: 0.6188 (Cg_exo) REVERT: V 58 ARG cc_start: 0.7072 (mmp80) cc_final: 0.6201 (ptp-170) REVERT: V 96 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8133 (pt0) REVERT: V 159 ARG cc_start: 0.7709 (tpp80) cc_final: 0.7438 (tpp80) REVERT: W 78 ASN cc_start: 0.8730 (m-40) cc_final: 0.8135 (t0) outliers start: 134 outliers final: 107 residues processed: 515 average time/residue: 0.3371 time to fit residues: 265.5736 Evaluate side-chains 523 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 411 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU 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 101 THR 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 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 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 138 VAL 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 33 ILE 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 64 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 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 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 K residue 71 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 121 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 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 196 VAL Chi-restraints excluded: chain O residue 109 TYR Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain 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 R residue 196 VAL 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 127 SER Chi-restraints excluded: chain T residue 167 ASP Chi-restraints excluded: chain U residue 22 THR 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 142 LEU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain W residue 31 LYS 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: 5.9990 chunk 138 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 46 optimal weight: 0.0670 chunk 59 optimal weight: 0.5980 chunk 185 optimal weight: 0.0020 chunk 263 optimal weight: 0.5980 chunk 170 optimal weight: 5.9990 chunk 271 optimal weight: 8.9990 overall best weight: 1.4528 ------------------------------------------------------------------------------- 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 40 ASN ** N 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.122987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.100119 restraints weight = 80976.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.103023 restraints weight = 54121.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.105134 restraints weight = 40345.902| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.8524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22444 Z= 0.136 Angle : 0.761 11.453 30566 Z= 0.372 Chirality : 0.049 0.345 3753 Planarity : 0.006 0.058 3918 Dihedral : 5.243 57.032 3088 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.71 % Allowed : 33.13 % Favored : 63.16 % 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: -0.05 (0.16), residues: 2862 helix: 1.27 (0.16), residues: 1044 sheet: -0.37 (0.19), residues: 756 loop : -1.00 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 112 HIS 0.005 0.001 HIS T 155 PHE 0.030 0.003 PHE M 115 TYR 0.019 0.001 TYR A 109 ARG 0.014 0.001 ARG T 141 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 1096) hydrogen bonds : angle 4.48781 ( 3153) covalent geometry : bond 0.00322 (22444) covalent geometry : angle 0.76102 (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 550 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 463 time to evaluate : 2.600 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: B 58 ARG cc_start: 0.7856 (mmp80) cc_final: 0.7420 (mmm160) REVERT: B 62 MET cc_start: 0.8396 (tpp) cc_final: 0.7877 (tpt) REVERT: B 116 ASP cc_start: 0.8254 (t0) cc_final: 0.7778 (p0) REVERT: C 54 LYS cc_start: 0.9113 (ttpp) cc_final: 0.8784 (ttpp) REVERT: D 24 ILE cc_start: 0.9012 (mp) cc_final: 0.8393 (tt) REVERT: E 31 LYS cc_start: 0.8646 (mttt) cc_final: 0.8435 (mmmt) REVERT: E 36 LYS cc_start: 0.8948 (mmtm) cc_final: 0.8198 (tptp) REVERT: E 41 ARG cc_start: 0.8009 (tpt-90) cc_final: 0.7562 (mmt180) REVERT: F 19 ARG cc_start: 0.7895 (mmt180) cc_final: 0.7563 (mmt180) REVERT: F 90 ASP cc_start: 0.7751 (m-30) cc_final: 0.7509 (m-30) REVERT: F 159 ARG cc_start: 0.7989 (tpp80) cc_final: 0.7723 (tpp80) REVERT: G 17 MET cc_start: 0.4315 (ttt) cc_final: 0.3947 (tpt) REVERT: G 36 LYS cc_start: 0.9187 (mmtm) cc_final: 0.8897 (tptp) REVERT: I 85 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6367 (m-80) REVERT: J 19 ARG cc_start: 0.9209 (mmt180) cc_final: 0.8540 (ppt170) REVERT: J 35 LYS cc_start: 0.9183 (tppp) cc_final: 0.8884 (tppt) REVERT: J 58 ARG cc_start: 0.6895 (mmp-170) cc_final: 0.6624 (mmp80) REVERT: J 62 MET cc_start: 0.6248 (tpp) cc_final: 0.5503 (tpp) REVERT: J 102 LEU cc_start: 0.8893 (mp) cc_final: 0.8155 (tt) REVERT: K 17 MET cc_start: 0.3967 (tpp) cc_final: 0.1443 (pmm) REVERT: K 37 LEU cc_start: 0.9091 (tp) cc_final: 0.8708 (mm) REVERT: K 41 ARG cc_start: 0.8877 (mtp85) cc_final: 0.8654 (ptm-80) REVERT: L 26 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7041 (mt-10) REVERT: L 74 MET cc_start: 0.9176 (mmp) cc_final: 0.8915 (mmt) REVERT: N 79 ASP cc_start: 0.9274 (t0) cc_final: 0.8983 (t0) REVERT: O 92 ASP cc_start: 0.7463 (m-30) cc_final: 0.6916 (t70) REVERT: O 109 TYR cc_start: 0.6741 (OUTLIER) cc_final: 0.5001 (t80) REVERT: R 58 ARG cc_start: 0.7661 (mmp-170) cc_final: 0.7108 (mmp80) REVERT: S 17 MET cc_start: 0.4106 (OUTLIER) cc_final: 0.3862 (mpp) REVERT: S 42 LEU cc_start: 0.8936 (mt) cc_final: 0.8614 (mt) REVERT: T 18 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7568 (mt-10) REVERT: T 69 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6844 (t0) REVERT: T 167 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8502 (t0) REVERT: T 169 GLU cc_start: 0.8551 (mp0) cc_final: 0.8142 (mp0) REVERT: V 19 ARG cc_start: 0.8194 (mtm-85) cc_final: 0.7696 (mpp80) REVERT: V 53 PRO cc_start: 0.6576 (Cg_endo) cc_final: 0.6223 (Cg_exo) REVERT: V 58 ARG cc_start: 0.7155 (mmp80) cc_final: 0.6300 (ptp-170) REVERT: V 96 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7976 (pt0) REVERT: V 159 ARG cc_start: 0.7638 (tpp80) cc_final: 0.7342 (tpp80) REVERT: W 78 ASN cc_start: 0.8676 (m-40) cc_final: 0.8101 (t0) outliers start: 87 outliers final: 66 residues processed: 522 average time/residue: 0.3385 time to fit residues: 271.0418 Evaluate side-chains 503 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 432 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 101 THR 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 29 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 64 LEU 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 79 VAL Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 100 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 109 TYR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 49 THR 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 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 93 LEU Chi-restraints excluded: chain T residue 167 ASP Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 142 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain W residue 31 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 74 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 chunk 254 optimal weight: 0.8980 chunk 260 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 279 optimal weight: 9.9990 chunk 174 optimal weight: 20.0000 chunk 270 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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** ** I 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.120886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.098099 restraints weight = 79979.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.100979 restraints weight = 53430.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.103080 restraints weight = 39814.294| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.8719 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= 0.155 Angle : 0.783 13.299 30566 Z= 0.383 Chirality : 0.049 0.308 3753 Planarity : 0.006 0.057 3918 Dihedral : 5.291 57.335 3088 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.41 % Allowed : 34.20 % Favored : 62.39 % 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: 1.18 (0.16), residues: 1044 sheet: -0.55 (0.18), residues: 783 loop : -0.88 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 112 HIS 0.010 0.001 HIS I 90 PHE 0.032 0.003 PHE O 115 TYR 0.021 0.001 TYR I 109 ARG 0.016 0.001 ARG L 179 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 1096) hydrogen bonds : angle 4.55813 ( 3153) covalent geometry : bond 0.00373 (22444) covalent geometry : angle 0.78266 (30566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8993.81 seconds wall clock time: 157 minutes 58.36 seconds (9478.36 seconds total)