Starting phenix.real_space_refine on Sun Aug 24 13:10:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j1l_61075/08_2025/9j1l_61075.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j1l_61075/08_2025/9j1l_61075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j1l_61075/08_2025/9j1l_61075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j1l_61075/08_2025/9j1l_61075.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j1l_61075/08_2025/9j1l_61075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j1l_61075/08_2025/9j1l_61075.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 69 5.16 5 C 12801 2.51 5 N 3363 2.21 5 O 4053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20288 Number of models: 1 Model: "" Number of chains: 17 Chain: "1" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1515 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain: "2" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1383 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 3, 'TRANS': 173} Chain: "3" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1098 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "A" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1383 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 3, 'TRANS': 173} Chain: "B" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1383 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 3, 'TRANS': 173} Chain: "C" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1383 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 3, 'TRANS': 173} Chain: "I" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1383 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 3, 'TRANS': 173} Chain: "N" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1515 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain: "O" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1098 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "P" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1383 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 3, 'TRANS': 173} Chain: "Q" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1383 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 3, 'TRANS': 173} Chain: "R" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1383 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 3, 'TRANS': 173} Chain: "n" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1515 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain: "o" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1098 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "p" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1383 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 3, 'TRANS': 173} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.33, per 1000 atoms: 0.26 Number of scatterers: 20288 At special positions: 0 Unit cell: (131.052, 164.353, 229.879, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 69 16.00 O 4053 8.00 N 3363 7.00 C 12801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 900.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4830 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 34 sheets defined 29.1% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain '1' and resid 14 through 73 removed outlier: 3.629A pdb=" N ARG 1 18 " --> pdb=" O GLY 1 14 " (cutoff:3.500A) Processing helix chain '1' and resid 95 through 108 Processing helix chain '1' and resid 116 through 121 removed outlier: 3.584A pdb=" N ILE 1 121 " --> pdb=" O ALA 1 117 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 26 No H-bonds generated for 'chain '2' and resid 24 through 26' Processing helix chain '2' and resid 37 through 45 Processing helix chain '2' and resid 49 through 72 removed outlier: 4.014A pdb=" N GLN 2 53 " --> pdb=" O ALA 2 49 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS 2 54 " --> pdb=" O GLY 2 50 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ALA 2 55 " --> pdb=" O ALA 2 51 " (cutoff:3.500A) Processing helix chain '2' and resid 125 through 131 Processing helix chain '3' and resid 24 through 28 Processing helix chain '3' and resid 30 through 37 Processing helix chain '3' and resid 81 through 91 removed outlier: 3.595A pdb=" N ASP 3 89 " --> pdb=" O LYS 3 85 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLN 3 90 " --> pdb=" O GLN 3 86 " (cutoff:3.500A) Processing helix chain '3' and resid 136 through 146 Processing helix chain 'A' and resid 37 through 45 removed outlier: 4.143A pdb=" N LYS A 45 " --> pdb=" O ILE A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'B' and resid 37 through 45 removed outlier: 4.273A pdb=" N GLN B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 45 " --> pdb=" O ILE B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 72 removed outlier: 3.609A pdb=" N GLY B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'C' and resid 37 through 45 removed outlier: 3.988A pdb=" N ILE C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.564A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 131 Processing helix chain 'I' and resid 36 through 45 Processing helix chain 'I' and resid 49 through 72 removed outlier: 3.902A pdb=" N GLN I 53 " --> pdb=" O ALA I 49 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS I 54 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ALA I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 95 removed outlier: 3.854A pdb=" N LYS I 94 " --> pdb=" O ASP I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 131 removed outlier: 4.188A pdb=" N GLU I 130 " --> pdb=" O ALA I 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 73 removed outlier: 3.588A pdb=" N ARG N 18 " --> pdb=" O GLY N 14 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP N 61 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS N 62 " --> pdb=" O ASP N 58 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA N 63 " --> pdb=" O THR N 59 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASN N 65 " --> pdb=" O ASP N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 85 Processing helix chain 'N' and resid 95 through 108 removed outlier: 3.819A pdb=" N ARG N 99 " --> pdb=" O VAL N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 116 through 122 removed outlier: 3.861A pdb=" N ILE N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER N 122 " --> pdb=" O SER N 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 28 Processing helix chain 'O' and resid 30 through 38 Processing helix chain 'O' and resid 81 through 91 removed outlier: 4.054A pdb=" N GLN O 90 " --> pdb=" O GLN O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'O' and resid 136 through 146 Processing helix chain 'P' and resid 37 through 45 Processing helix chain 'P' and resid 47 through 72 Processing helix chain 'P' and resid 125 through 131 removed outlier: 3.815A pdb=" N GLU P 130 " --> pdb=" O ALA P 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 45 removed outlier: 4.244A pdb=" N GLN Q 44 " --> pdb=" O THR Q 40 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS Q 45 " --> pdb=" O ILE Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 72 Processing helix chain 'Q' and resid 125 through 129 Processing helix chain 'Q' and resid 130 through 132 No H-bonds generated for 'chain 'Q' and resid 130 through 132' Processing helix chain 'Q' and resid 163 through 167 removed outlier: 3.553A pdb=" N TYR Q 167 " --> pdb=" O ASN Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 45 removed outlier: 4.059A pdb=" N ILE R 41 " --> pdb=" O GLU R 37 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP R 42 " --> pdb=" O GLU R 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 72 removed outlier: 3.625A pdb=" N ILE R 69 " --> pdb=" O TYR R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 131 Processing helix chain 'n' and resid 14 through 72 Processing helix chain 'n' and resid 79 through 84 Processing helix chain 'n' and resid 95 through 108 Processing helix chain 'n' and resid 117 through 122 removed outlier: 4.069A pdb=" N ILE n 121 " --> pdb=" O ALA n 117 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER n 122 " --> pdb=" O SER n 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 117 through 122' Processing helix chain 'o' and resid 30 through 38 Processing helix chain 'o' and resid 57 through 61 Processing helix chain 'o' and resid 81 through 92 Processing helix chain 'o' and resid 136 through 146 Processing helix chain 'p' and resid 37 through 45 removed outlier: 3.725A pdb=" N ILE p 41 " --> pdb=" O GLU p 37 " (cutoff:3.500A) Processing helix chain 'p' and resid 47 through 72 Processing helix chain 'p' and resid 91 through 95 Processing helix chain 'p' and resid 125 through 131 Processing sheet with id=AA1, first strand: chain '1' and resid 113 through 114 removed outlier: 7.293A pdb=" N GLN 1 114 " --> pdb=" O LEU 1 130 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N THR 1 132 " --> pdb=" O GLN 1 114 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 128 through 135 current: chain 'O' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 16 through 18 current: chain 'n' and resid 173 through 176 WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 173 through 176 current: chain 'o' and resid 16 through 21 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '1' and resid 141 through 142 removed outlier: 6.482A pdb=" N THR 1 141 " --> pdb=" O VAL 1 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 173 through 175 current: chain '3' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 16 through 18 current: chain 'N' and resid 128 through 134 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '1' and resid 147 through 148 removed outlier: 7.249A pdb=" N SER 1 148 " --> pdb=" O LEU 1 158 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N LYS 1 160 " --> pdb=" O SER 1 148 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE 1 156 " --> pdb=" O LYS 2 10 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LYS 2 10 " --> pdb=" O ILE 1 156 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU 1 158 " --> pdb=" O SER 2 8 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N SER 2 8 " --> pdb=" O LEU 1 158 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LYS 1 160 " --> pdb=" O LYS 2 6 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LYS 2 6 " --> pdb=" O LYS 1 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '2' and resid 15 through 18 current: chain 'P' and resid 16 through 21 Processing sheet with id=AA4, first strand: chain '1' and resid 184 through 188 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 184 through 188 current: chain 'p' and resid 4 through 10 Processing sheet with id=AA5, first strand: chain '2' and resid 28 through 29 Processing sheet with id=AA6, first strand: chain '2' and resid 73 through 80 removed outlier: 7.338A pdb=" N PHE 2 76 " --> pdb=" O THR 2 176 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR 2 176 " --> pdb=" O PHE 2 76 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY 2 78 " --> pdb=" O GLN 2 174 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLN 2 174 " --> pdb=" O GLY 2 78 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU 2 102 " --> pdb=" O ARG 2 173 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL 2 175 " --> pdb=" O THR 2 100 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR 2 100 " --> pdb=" O VAL 2 175 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE 2 177 " --> pdb=" O GLY 2 98 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY 2 98 " --> pdb=" O ILE 2 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 87 through 89 Processing sheet with id=AA8, first strand: chain '3' and resid 45 through 46 removed outlier: 6.213A pdb=" N SER 3 45 " --> pdb=" O VAL o 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain '3' and resid 52 through 53 Processing sheet with id=AB1, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.492A pdb=" N LYS A 3 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY N 162 " --> pdb=" O ILE A 4 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 8 through 10 removed outlier: 3.900A pdb=" N LYS C 3 " --> pdb=" O GLN A 18 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 16 through 18 current: chain 'N' and resid 156 through 157 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 156 through 157 current: chain 'N' and resid 184 through 188 Processing sheet with id=AB3, first strand: chain 'A' and resid 73 through 80 removed outlier: 3.714A pdb=" N ILE A 75 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL A 175 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LYS A 77 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N ARG A 173 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ALA A 79 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N ALA A 171 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU A 172 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N SER A 104 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 105 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TYR A 117 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR A 116 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU B 137 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR A 118 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AB6, first strand: chain 'B' and resid 73 through 76 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 73 through 76 current: chain 'B' and resid 119 through 124 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 73 through 80 removed outlier: 5.182A pdb=" N VAL C 74 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE C 177 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG C 173 " --> pdb=" O GLY C 78 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN C 80 " --> pdb=" O ALA C 171 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ALA C 171 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU C 102 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL C 175 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR C 100 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE C 177 " --> pdb=" O GLY C 98 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLY C 98 " --> pdb=" O ILE C 177 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 87 through 89 Processing sheet with id=AB9, first strand: chain 'I' and resid 3 through 10 removed outlier: 11.691A pdb=" N VAL I 5 " --> pdb=" O PRO I 21 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N MET I 7 " --> pdb=" O PHE I 19 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 16 through 21 current: chain 'Q' and resid 16 through 20 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 16 through 20 current: chain 'R' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 16 through 18 current: chain 'n' and resid 156 through 163 Processing sheet with id=AC1, first strand: chain 'I' and resid 74 through 80 removed outlier: 6.193A pdb=" N VAL I 74 " --> pdb=" O ILE I 177 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE I 177 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE I 76 " --> pdb=" O VAL I 175 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG I 173 " --> pdb=" O GLY I 78 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN I 80 " --> pdb=" O ALA I 171 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ALA I 171 " --> pdb=" O ASN I 80 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA I 171 " --> pdb=" O SER I 104 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU I 102 " --> pdb=" O ARG I 173 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL I 175 " --> pdb=" O THR I 100 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR I 100 " --> pdb=" O VAL I 175 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG I 105 " --> pdb=" O TYR I 117 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N TYR I 117 " --> pdb=" O ARG I 105 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 87 through 89 Processing sheet with id=AC3, first strand: chain 'O' and resid 52 through 53 Processing sheet with id=AC4, first strand: chain 'P' and resid 4 through 5 Processing sheet with id=AC5, first strand: chain 'P' and resid 23 through 24 removed outlier: 7.640A pdb=" N THR P 23 " --> pdb=" O LYS p 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'P' and resid 73 through 80 removed outlier: 9.981A pdb=" N VAL P 74 " --> pdb=" O MET P 178 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N MET P 178 " --> pdb=" O VAL P 74 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N PHE P 76 " --> pdb=" O THR P 176 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N THR P 176 " --> pdb=" O PHE P 76 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLY P 78 " --> pdb=" O GLN P 174 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN P 174 " --> pdb=" O GLY P 78 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU P 102 " --> pdb=" O ARG P 173 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL P 175 " --> pdb=" O THR P 100 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR P 100 " --> pdb=" O VAL P 175 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE P 177 " --> pdb=" O GLY P 98 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY P 98 " --> pdb=" O ILE P 177 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 87 through 89 Processing sheet with id=AC8, first strand: chain 'P' and resid 136 through 139 Processing sheet with id=AC9, first strand: chain 'Q' and resid 4 through 5 Processing sheet with id=AD1, first strand: chain 'Q' and resid 73 through 80 removed outlier: 5.315A pdb=" N VAL Q 74 " --> pdb=" O ILE Q 177 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE Q 177 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG Q 173 " --> pdb=" O GLY Q 78 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN Q 80 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ALA Q 171 " --> pdb=" O ASN Q 80 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU Q 102 " --> pdb=" O ARG Q 173 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL Q 175 " --> pdb=" O THR Q 100 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR Q 100 " --> pdb=" O VAL Q 175 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE Q 177 " --> pdb=" O GLY Q 98 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY Q 98 " --> pdb=" O ILE Q 177 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 87 through 89 Processing sheet with id=AD3, first strand: chain 'Q' and resid 136 through 139 Processing sheet with id=AD4, first strand: chain 'R' and resid 73 through 77 removed outlier: 6.623A pdb=" N VAL R 175 " --> pdb=" O ILE R 75 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LYS R 77 " --> pdb=" O ARG R 173 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ARG R 173 " --> pdb=" O LYS R 77 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU R 172 " --> pdb=" O SER R 104 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N SER R 104 " --> pdb=" O LEU R 172 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 87 through 89 Processing sheet with id=AD6, first strand: chain 'p' and resid 73 through 80 removed outlier: 5.294A pdb=" N VAL p 74 " --> pdb=" O ILE p 177 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE p 177 " --> pdb=" O VAL p 74 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG p 173 " --> pdb=" O GLY p 78 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN p 80 " --> pdb=" O ALA p 171 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ALA p 171 " --> pdb=" O ASN p 80 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU p 172 " --> pdb=" O SER p 104 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N SER p 104 " --> pdb=" O LEU p 172 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'p' and resid 88 through 89 removed outlier: 3.599A pdb=" N TYR p 152 " --> pdb=" O SER p 159 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3517 1.31 - 1.43: 5464 1.43 - 1.56: 11540 1.56 - 1.68: 3 1.68 - 1.81: 134 Bond restraints: 20658 Sorted by residual: bond pdb=" CB ILE A 177 " pdb=" CG1 ILE A 177 " ideal model delta sigma weight residual 1.530 1.425 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" N MET C 140 " pdb=" CA MET C 140 " ideal model delta sigma weight residual 1.452 1.519 -0.067 1.46e-02 4.69e+03 2.11e+01 bond pdb=" SD MET Q 140 " pdb=" CE MET Q 140 " ideal model delta sigma weight residual 1.791 1.677 0.114 2.50e-02 1.60e+03 2.09e+01 bond pdb=" CZ ARG C 148 " pdb=" NH2 ARG C 148 " ideal model delta sigma weight residual 1.330 1.272 0.058 1.30e-02 5.92e+03 2.02e+01 bond pdb=" CB ILE A 75 " pdb=" CG1 ILE A 75 " ideal model delta sigma weight residual 1.530 1.449 0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 20653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 27693 2.65 - 5.30: 191 5.30 - 7.96: 25 7.96 - 10.61: 5 10.61 - 13.26: 1 Bond angle restraints: 27915 Sorted by residual: angle pdb=" CA MET C 140 " pdb=" C MET C 140 " pdb=" O MET C 140 " ideal model delta sigma weight residual 120.88 113.91 6.97 1.12e+00 7.97e-01 3.87e+01 angle pdb=" CA MET C 140 " pdb=" C MET C 140 " pdb=" N PRO C 141 " ideal model delta sigma weight residual 117.48 124.27 -6.79 1.15e+00 7.56e-01 3.48e+01 angle pdb=" N GLU p 26 " pdb=" CA GLU p 26 " pdb=" C GLU p 26 " ideal model delta sigma weight residual 114.62 108.22 6.40 1.14e+00 7.69e-01 3.15e+01 angle pdb=" C LYS R 45 " pdb=" CA LYS R 45 " pdb=" CB LYS R 45 " ideal model delta sigma weight residual 116.54 110.44 6.10 1.15e+00 7.56e-01 2.81e+01 angle pdb=" C ALA 3 96 " pdb=" CA ALA 3 96 " pdb=" CB ALA 3 96 " ideal model delta sigma weight residual 115.79 109.82 5.97 1.19e+00 7.06e-01 2.52e+01 ... (remaining 27910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10342 17.97 - 35.93: 1491 35.93 - 53.90: 354 53.90 - 71.86: 76 71.86 - 89.83: 34 Dihedral angle restraints: 12297 sinusoidal: 4773 harmonic: 7524 Sorted by residual: dihedral pdb=" CA VAL C 34 " pdb=" C VAL C 34 " pdb=" N SER C 35 " pdb=" CA SER C 35 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ASN o 14 " pdb=" C ASN o 14 " pdb=" N SER o 15 " pdb=" CA SER o 15 " ideal model delta harmonic sigma weight residual -180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA VAL 2 5 " pdb=" C VAL 2 5 " pdb=" N LYS 2 6 " pdb=" CA LYS 2 6 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 12294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3043 0.100 - 0.201: 86 0.201 - 0.301: 2 0.301 - 0.401: 0 0.401 - 0.502: 1 Chirality restraints: 3132 Sorted by residual: chirality pdb=" CG LEU B 131 " pdb=" CB LEU B 131 " pdb=" CD1 LEU B 131 " pdb=" CD2 LEU B 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.29e+00 chirality pdb=" CA MET C 140 " pdb=" N MET C 140 " pdb=" C MET C 140 " pdb=" CB MET C 140 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE A 177 " pdb=" CA ILE A 177 " pdb=" CG1 ILE A 177 " pdb=" CG2 ILE A 177 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3129 not shown) Planarity restraints: 3564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 140 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C MET C 140 " -0.054 2.00e-02 2.50e+03 pdb=" O MET C 140 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO C 141 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 166 " -0.017 2.00e-02 2.50e+03 2.06e-02 7.40e+00 pdb=" CG PHE N 166 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE N 166 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE N 166 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE N 166 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 166 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE N 166 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 117 " -0.019 2.00e-02 2.50e+03 1.76e-02 6.21e+00 pdb=" CG TYR B 117 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR B 117 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 117 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR B 117 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR B 117 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 117 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR B 117 " -0.020 2.00e-02 2.50e+03 ... (remaining 3561 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 471 2.65 - 3.21: 19684 3.21 - 3.78: 32813 3.78 - 4.34: 44456 4.34 - 4.90: 71558 Nonbonded interactions: 168982 Sorted by model distance: nonbonded pdb=" O ASP N 61 " pdb=" OD1 ASP N 61 " model vdw 2.090 3.040 nonbonded pdb=" OD1 ASP O 89 " pdb=" N GLN O 90 " model vdw 2.102 3.120 nonbonded pdb=" OG1 THR 2 100 " pdb=" OG1 THR 2 176 " model vdw 2.106 3.040 nonbonded pdb=" OD1 ASP R 115 " pdb=" OH TYR R 118 " model vdw 2.159 3.040 nonbonded pdb=" OH TYR A 106 " pdb=" OD1 ASN A 111 " model vdw 2.176 3.040 ... (remaining 168977 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 '1' selection = chain 'N' selection = chain 'n' } ncs_group { reference = chain '2' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'I' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'p' } ncs_group { reference = (chain '3' and resid 2 through 146) selection = chain 'O' selection = (chain 'o' and resid 2 through 146) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 19.900 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 : 0.004 0.114 20658 Z= 0.183 Angle : 0.612 13.261 27915 Z= 0.341 Chirality : 0.041 0.502 3132 Planarity : 0.003 0.034 3564 Dihedral : 18.178 89.828 7467 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.00 % Favored : 93.42 % Rotamer: Outliers : 0.27 % Allowed : 31.64 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.16), residues: 2568 helix: 1.65 (0.20), residues: 713 sheet: -0.62 (0.26), residues: 404 loop : -1.44 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG p 173 TYR 0.030 0.001 TYR B 117 PHE 0.047 0.002 PHE N 166 TRP 0.042 0.002 TRP B 42 HIS 0.003 0.001 HIS Q 13 Details of bonding type rmsd covalent geometry : bond 0.00391 (20658) covalent geometry : angle 0.61211 (27915) hydrogen bonds : bond 0.13862 ( 695) hydrogen bonds : angle 5.50184 ( 1974) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 100 THR cc_start: -0.0566 (OUTLIER) cc_final: -0.1205 (p) outliers start: 6 outliers final: 3 residues processed: 198 average time/residue: 0.1354 time to fit residues: 43.8278 Evaluate side-chains 198 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 194 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain p residue 53 GLN Chi-restraints excluded: chain p residue 74 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 50.0000 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0010 overall best weight: 3.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 127 GLN A 56 ASN A 114 GLN C 18 GLN ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 161 HIS o 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.164800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.103650 restraints weight = 46345.983| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.03 r_work: 0.3313 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20658 Z= 0.183 Angle : 0.587 10.087 27915 Z= 0.313 Chirality : 0.041 0.161 3132 Planarity : 0.003 0.036 3564 Dihedral : 4.615 43.585 2758 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.17 % Favored : 92.25 % Rotamer: Outliers : 3.84 % Allowed : 28.58 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.16), residues: 2568 helix: 1.39 (0.20), residues: 739 sheet: -0.86 (0.26), residues: 390 loop : -1.55 (0.15), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 148 TYR 0.022 0.002 TYR 1 45 PHE 0.027 0.002 PHE 1 17 TRP 0.024 0.002 TRP B 42 HIS 0.005 0.001 HIS Q 13 Details of bonding type rmsd covalent geometry : bond 0.00427 (20658) covalent geometry : angle 0.58690 (27915) hydrogen bonds : bond 0.04600 ( 695) hydrogen bonds : angle 4.69655 ( 1974) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 201 time to evaluate : 0.745 Fit side-chains REVERT: 1 71 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7976 (mm) REVERT: A 99 MET cc_start: 0.2150 (pmm) cc_final: 0.1515 (ptp) REVERT: B 140 MET cc_start: 0.4614 (mpp) cc_final: 0.3874 (ttp) REVERT: B 148 ARG cc_start: 0.3952 (OUTLIER) cc_final: 0.3563 (pmt-80) REVERT: C 11 ASN cc_start: 0.8263 (m-40) cc_final: 0.7832 (m-40) REVERT: C 148 ARG cc_start: 0.2155 (ttp-170) cc_final: 0.1764 (ttp-170) REVERT: n 9 GLU cc_start: 0.8573 (mp0) cc_final: 0.8319 (mm-30) REVERT: p 56 ASN cc_start: 0.8675 (t0) cc_final: 0.8468 (t0) REVERT: p 130 GLU cc_start: 0.8430 (tp30) cc_final: 0.8124 (tp30) outliers start: 84 outliers final: 39 residues processed: 269 average time/residue: 0.1393 time to fit residues: 60.4714 Evaluate side-chains 224 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 112 THR Chi-restraints excluded: chain 1 residue 128 ILE Chi-restraints excluded: chain 1 residue 155 ASP Chi-restraints excluded: chain 1 residue 161 THR Chi-restraints excluded: chain 2 residue 33 SER Chi-restraints excluded: chain 2 residue 66 VAL Chi-restraints excluded: chain 2 residue 127 GLN Chi-restraints excluded: chain 2 residue 128 LEU Chi-restraints excluded: chain 2 residue 176 THR Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 59 ASP Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 80 MET Chi-restraints excluded: chain O residue 83 PHE Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 147 ASP Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain o residue 43 VAL Chi-restraints excluded: chain p residue 31 LEU Chi-restraints excluded: chain p residue 74 VAL Chi-restraints excluded: chain p residue 140 MET Chi-restraints excluded: chain p residue 175 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 214 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 179 optimal weight: 30.0000 chunk 171 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 90 optimal weight: 30.0000 chunk 113 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.164229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.102953 restraints weight = 46372.902| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.29 r_work: 0.3295 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20658 Z= 0.185 Angle : 0.572 8.220 27915 Z= 0.305 Chirality : 0.041 0.174 3132 Planarity : 0.003 0.034 3564 Dihedral : 4.674 57.780 2754 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.54 % Favored : 92.87 % Rotamer: Outliers : 4.02 % Allowed : 29.08 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.16), residues: 2568 helix: 1.36 (0.20), residues: 735 sheet: -0.85 (0.26), residues: 395 loop : -1.62 (0.15), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 148 TYR 0.018 0.001 TYR 1 45 PHE 0.038 0.002 PHE N 166 TRP 0.014 0.002 TRP Q 42 HIS 0.005 0.001 HIS Q 13 Details of bonding type rmsd covalent geometry : bond 0.00435 (20658) covalent geometry : angle 0.57173 (27915) hydrogen bonds : bond 0.04564 ( 695) hydrogen bonds : angle 4.58494 ( 1974) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 192 time to evaluate : 0.769 Fit side-chains REVERT: 1 71 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7952 (mm) REVERT: A 99 MET cc_start: 0.1860 (pmm) cc_final: 0.1261 (ptp) REVERT: B 140 MET cc_start: 0.4729 (mpp) cc_final: 0.4019 (ttp) REVERT: B 148 ARG cc_start: 0.4111 (OUTLIER) cc_final: 0.3777 (pmt-80) REVERT: B 178 MET cc_start: 0.3466 (pmm) cc_final: 0.3166 (ptt) REVERT: C 11 ASN cc_start: 0.8215 (m-40) cc_final: 0.7793 (m-40) REVERT: C 17 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.5434 (mp0) REVERT: C 148 ARG cc_start: 0.2319 (ttp-170) cc_final: 0.1837 (ttp-170) REVERT: I 7 MET cc_start: 0.8520 (mtp) cc_final: 0.8074 (mtp) REVERT: O 58 GLU cc_start: 0.9121 (tp30) cc_final: 0.8906 (tp30) REVERT: P 162 PHE cc_start: 0.8366 (t80) cc_final: 0.8096 (t80) REVERT: Q 140 MET cc_start: -0.0012 (ttm) cc_final: -0.0696 (ttm) REVERT: R 94 LYS cc_start: 0.1774 (mttm) cc_final: 0.1471 (tptt) REVERT: p 56 ASN cc_start: 0.8693 (t0) cc_final: 0.8428 (t0) outliers start: 88 outliers final: 56 residues processed: 258 average time/residue: 0.1385 time to fit residues: 57.9876 Evaluate side-chains 245 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 186 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 42 ILE Chi-restraints excluded: chain 1 residue 57 ILE Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 112 THR Chi-restraints excluded: chain 1 residue 128 ILE Chi-restraints excluded: chain 1 residue 155 ASP Chi-restraints excluded: chain 1 residue 161 THR Chi-restraints excluded: chain 2 residue 33 SER Chi-restraints excluded: chain 2 residue 127 GLN Chi-restraints excluded: chain 2 residue 136 ILE Chi-restraints excluded: chain 2 residue 176 THR Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 59 ASP Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 80 MET Chi-restraints excluded: chain O residue 83 PHE Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 147 ASP Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 140 MET Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain n residue 130 LEU Chi-restraints excluded: chain n residue 134 LYS Chi-restraints excluded: chain n residue 141 THR Chi-restraints excluded: chain n residue 164 THR Chi-restraints excluded: chain o residue 43 VAL Chi-restraints excluded: chain o residue 101 ILE Chi-restraints excluded: chain p residue 5 VAL Chi-restraints excluded: chain p residue 12 GLU Chi-restraints excluded: chain p residue 31 LEU Chi-restraints excluded: chain p residue 41 ILE Chi-restraints excluded: chain p residue 74 VAL Chi-restraints excluded: chain p residue 112 THR Chi-restraints excluded: chain p residue 138 VAL Chi-restraints excluded: chain p residue 140 MET Chi-restraints excluded: chain p residue 175 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 96 optimal weight: 20.0000 chunk 65 optimal weight: 40.0000 chunk 156 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 194 optimal weight: 40.0000 chunk 120 optimal weight: 1.9990 chunk 180 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 72 optimal weight: 50.0000 chunk 103 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 127 GLN ** 3 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.161125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.105033 restraints weight = 46316.860| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 4.20 r_work: 0.3207 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 20658 Z= 0.323 Angle : 0.687 9.591 27915 Z= 0.368 Chirality : 0.045 0.173 3132 Planarity : 0.004 0.052 3564 Dihedral : 5.244 57.290 2754 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.94 % Favored : 91.43 % Rotamer: Outliers : 6.49 % Allowed : 28.03 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.16), residues: 2568 helix: 0.92 (0.20), residues: 732 sheet: -1.02 (0.26), residues: 376 loop : -1.82 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 105 TYR 0.024 0.002 TYR 1 45 PHE 0.040 0.002 PHE N 166 TRP 0.047 0.002 TRP B 42 HIS 0.008 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00763 (20658) covalent geometry : angle 0.68719 (27915) hydrogen bonds : bond 0.05341 ( 695) hydrogen bonds : angle 4.97385 ( 1974) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 199 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: 1 71 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7979 (mm) REVERT: 1 185 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8132 (mt0) REVERT: 3 52 ARG cc_start: 0.7553 (mmm160) cc_final: 0.7233 (mmm160) REVERT: 3 58 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7822 (tp30) REVERT: 3 84 ASP cc_start: 0.8561 (m-30) cc_final: 0.8282 (m-30) REVERT: B 140 MET cc_start: 0.4349 (mpp) cc_final: 0.3684 (ttp) REVERT: B 148 ARG cc_start: 0.4496 (OUTLIER) cc_final: 0.4078 (pmt-80) REVERT: B 178 MET cc_start: 0.3228 (pmm) cc_final: 0.2735 (ptt) REVERT: C 24 HIS cc_start: 0.8201 (OUTLIER) cc_final: 0.7503 (t70) REVERT: C 86 GLN cc_start: 0.2663 (OUTLIER) cc_final: 0.2351 (mp10) REVERT: C 148 ARG cc_start: 0.2655 (ttp-170) cc_final: 0.2260 (ttp-170) REVERT: I 7 MET cc_start: 0.8694 (mtp) cc_final: 0.8341 (mtp) REVERT: N 18 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6230 (ttm-80) REVERT: N 58 ASP cc_start: 0.8018 (t0) cc_final: 0.7755 (t0) REVERT: O 58 GLU cc_start: 0.9179 (tp30) cc_final: 0.8939 (tp30) REVERT: O 83 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7729 (p90) REVERT: P 114 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8203 (pm20) REVERT: Q 140 MET cc_start: -0.0975 (ttm) cc_final: -0.1244 (ttm) REVERT: R 10 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8032 (ptpp) REVERT: R 94 LYS cc_start: 0.1895 (mttm) cc_final: 0.1584 (tptt) REVERT: p 56 ASN cc_start: 0.8764 (t0) cc_final: 0.8460 (t0) outliers start: 142 outliers final: 84 residues processed: 313 average time/residue: 0.1281 time to fit residues: 64.8220 Evaluate side-chains 282 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 189 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 ILE Chi-restraints excluded: chain 1 residue 50 ASP Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 112 THR Chi-restraints excluded: chain 1 residue 128 ILE Chi-restraints excluded: chain 1 residue 133 SER Chi-restraints excluded: chain 1 residue 150 LEU Chi-restraints excluded: chain 1 residue 155 ASP Chi-restraints excluded: chain 1 residue 161 THR Chi-restraints excluded: chain 1 residue 185 GLN Chi-restraints excluded: chain 2 residue 33 SER Chi-restraints excluded: chain 2 residue 73 THR Chi-restraints excluded: chain 2 residue 95 LEU Chi-restraints excluded: chain 2 residue 127 GLN Chi-restraints excluded: chain 2 residue 136 ILE Chi-restraints excluded: chain 2 residue 140 MET Chi-restraints excluded: chain 2 residue 144 THR Chi-restraints excluded: chain 2 residue 155 THR Chi-restraints excluded: chain 2 residue 176 THR Chi-restraints excluded: chain 3 residue 10 THR Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 59 ASP Chi-restraints excluded: chain 3 residue 76 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 106 TYR Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 80 MET Chi-restraints excluded: chain O residue 83 PHE Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain P residue 114 GLN Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 147 ASP Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 140 MET Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain n residue 95 VAL Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain n residue 130 LEU Chi-restraints excluded: chain n residue 134 LYS Chi-restraints excluded: chain n residue 141 THR Chi-restraints excluded: chain n residue 147 ILE Chi-restraints excluded: chain n residue 157 VAL Chi-restraints excluded: chain n residue 164 THR Chi-restraints excluded: chain n residue 173 LEU Chi-restraints excluded: chain o residue 15 SER Chi-restraints excluded: chain o residue 25 VAL Chi-restraints excluded: chain o residue 43 VAL Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain o residue 101 ILE Chi-restraints excluded: chain p residue 12 GLU Chi-restraints excluded: chain p residue 28 VAL Chi-restraints excluded: chain p residue 31 LEU Chi-restraints excluded: chain p residue 41 ILE Chi-restraints excluded: chain p residue 74 VAL Chi-restraints excluded: chain p residue 99 MET Chi-restraints excluded: chain p residue 112 THR Chi-restraints excluded: chain p residue 136 ILE Chi-restraints excluded: chain p residue 140 MET Chi-restraints excluded: chain p residue 175 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 206 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 203 optimal weight: 0.2980 chunk 80 optimal weight: 40.0000 chunk 46 optimal weight: 40.0000 chunk 148 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 127 GLN I 13 HIS ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** o 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.163997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.103273 restraints weight = 46320.155| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.05 r_work: 0.3307 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20658 Z= 0.143 Angle : 0.558 8.676 27915 Z= 0.298 Chirality : 0.040 0.161 3132 Planarity : 0.003 0.033 3564 Dihedral : 4.787 58.131 2754 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.23 % Favored : 93.15 % Rotamer: Outliers : 4.66 % Allowed : 29.40 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.16), residues: 2568 helix: 1.29 (0.20), residues: 734 sheet: -0.89 (0.27), residues: 379 loop : -1.68 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 173 TYR 0.017 0.001 TYR A 118 PHE 0.023 0.001 PHE N 175 TRP 0.043 0.002 TRP B 42 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00327 (20658) covalent geometry : angle 0.55772 (27915) hydrogen bonds : bond 0.04436 ( 695) hydrogen bonds : angle 4.54150 ( 1974) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 204 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: 1 29 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8553 (mtm) REVERT: 1 57 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8654 (mt) REVERT: 1 71 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8032 (mm) REVERT: 3 52 ARG cc_start: 0.7415 (mmm160) cc_final: 0.7201 (mmm160) REVERT: 3 58 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7824 (tp30) REVERT: 3 64 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7146 (mmtt) REVERT: 3 84 ASP cc_start: 0.8497 (m-30) cc_final: 0.8228 (m-30) REVERT: A 82 MET cc_start: 0.3771 (mtm) cc_final: 0.3564 (mtm) REVERT: A 99 MET cc_start: 0.2139 (pmm) cc_final: 0.1596 (ptp) REVERT: B 81 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5632 (mp) REVERT: B 140 MET cc_start: 0.4388 (mpp) cc_final: 0.4027 (ttp) REVERT: B 148 ARG cc_start: 0.4211 (OUTLIER) cc_final: 0.3889 (pmt-80) REVERT: P 162 PHE cc_start: 0.8489 (t80) cc_final: 0.8204 (t80) REVERT: Q 63 LYS cc_start: 0.2243 (OUTLIER) cc_final: 0.1802 (mtpt) REVERT: Q 140 MET cc_start: 0.0087 (ttm) cc_final: -0.0741 (ttm) REVERT: Q 147 ASP cc_start: 0.4132 (OUTLIER) cc_final: 0.3746 (m-30) REVERT: R 94 LYS cc_start: 0.1859 (mttm) cc_final: 0.1592 (tptt) REVERT: o 95 GLU cc_start: 0.5771 (pm20) cc_final: 0.5570 (pp20) REVERT: p 56 ASN cc_start: 0.8776 (t0) cc_final: 0.8478 (t0) REVERT: p 82 MET cc_start: 0.9024 (tpp) cc_final: 0.8628 (mmm) REVERT: p 114 GLN cc_start: 0.7172 (mt0) cc_final: 0.6936 (mt0) outliers start: 102 outliers final: 69 residues processed: 283 average time/residue: 0.1420 time to fit residues: 64.5905 Evaluate side-chains 271 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 194 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 LEU Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 42 ILE Chi-restraints excluded: chain 1 residue 53 LEU Chi-restraints excluded: chain 1 residue 57 ILE Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 112 THR Chi-restraints excluded: chain 1 residue 133 SER Chi-restraints excluded: chain 1 residue 150 LEU Chi-restraints excluded: chain 1 residue 155 ASP Chi-restraints excluded: chain 2 residue 33 SER Chi-restraints excluded: chain 2 residue 73 THR Chi-restraints excluded: chain 2 residue 136 ILE Chi-restraints excluded: chain 2 residue 155 THR Chi-restraints excluded: chain 2 residue 176 THR Chi-restraints excluded: chain 3 residue 11 LYS Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 64 LYS Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 106 TYR Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 80 MET Chi-restraints excluded: chain O residue 83 PHE Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 147 ASP Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 140 MET Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain n residue 95 VAL Chi-restraints excluded: chain n residue 130 LEU Chi-restraints excluded: chain n residue 141 THR Chi-restraints excluded: chain o residue 15 SER Chi-restraints excluded: chain o residue 22 GLU Chi-restraints excluded: chain o residue 43 VAL Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain o residue 101 ILE Chi-restraints excluded: chain p residue 12 GLU Chi-restraints excluded: chain p residue 31 LEU Chi-restraints excluded: chain p residue 41 ILE Chi-restraints excluded: chain p residue 74 VAL Chi-restraints excluded: chain p residue 112 THR Chi-restraints excluded: chain p residue 136 ILE Chi-restraints excluded: chain p residue 138 VAL Chi-restraints excluded: chain p residue 155 THR Chi-restraints excluded: chain p residue 175 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 236 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 231 optimal weight: 0.0470 chunk 123 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 overall best weight: 3.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.163106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.102251 restraints weight = 45957.600| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.04 r_work: 0.3287 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20658 Z= 0.191 Angle : 0.579 8.713 27915 Z= 0.308 Chirality : 0.041 0.165 3132 Planarity : 0.003 0.031 3564 Dihedral : 4.812 58.468 2754 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.17 % Favored : 92.21 % Rotamer: Outliers : 5.72 % Allowed : 28.99 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.16), residues: 2568 helix: 1.20 (0.20), residues: 742 sheet: -0.91 (0.26), residues: 382 loop : -1.71 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 173 TYR 0.021 0.002 TYR 1 45 PHE 0.045 0.002 PHE N 166 TRP 0.039 0.002 TRP B 42 HIS 0.006 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00449 (20658) covalent geometry : angle 0.57936 (27915) hydrogen bonds : bond 0.04546 ( 695) hydrogen bonds : angle 4.59338 ( 1974) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 199 time to evaluate : 0.834 Fit side-chains REVERT: 1 71 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7992 (mm) REVERT: 1 185 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8300 (mt0) REVERT: 3 52 ARG cc_start: 0.7396 (mmm160) cc_final: 0.7170 (mmm160) REVERT: 3 58 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7851 (tp30) REVERT: 3 64 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7277 (mmtt) REVERT: 3 84 ASP cc_start: 0.8468 (m-30) cc_final: 0.8200 (m-30) REVERT: A 73 THR cc_start: 0.4854 (OUTLIER) cc_final: 0.4576 (t) REVERT: A 99 MET cc_start: 0.2270 (pmm) cc_final: 0.1596 (ptp) REVERT: A 177 ILE cc_start: 0.5131 (OUTLIER) cc_final: 0.4409 (mp) REVERT: B 35 SER cc_start: 0.7428 (t) cc_final: 0.7156 (p) REVERT: B 81 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5731 (mp) REVERT: B 140 MET cc_start: 0.4556 (mpp) cc_final: 0.3986 (ttp) REVERT: B 148 ARG cc_start: 0.4309 (ptt-90) cc_final: 0.3990 (pmt-80) REVERT: C 24 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7536 (t70) REVERT: I 131 LEU cc_start: 0.1427 (OUTLIER) cc_final: 0.1062 (tp) REVERT: N 18 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.6012 (ttm-80) REVERT: N 186 MET cc_start: 0.6785 (mtt) cc_final: 0.6528 (mtm) REVERT: O 9 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8592 (pp30) REVERT: Q 63 LYS cc_start: 0.2284 (OUTLIER) cc_final: 0.1856 (mtmt) REVERT: Q 140 MET cc_start: 0.0157 (ttm) cc_final: -0.0599 (ttm) REVERT: Q 147 ASP cc_start: 0.4119 (OUTLIER) cc_final: 0.3727 (m-30) REVERT: R 94 LYS cc_start: 0.2089 (mttm) cc_final: 0.1838 (tptp) REVERT: o 95 GLU cc_start: 0.5801 (pm20) cc_final: 0.5580 (pp20) REVERT: p 56 ASN cc_start: 0.8784 (t0) cc_final: 0.8480 (t0) REVERT: p 82 MET cc_start: 0.9064 (tpp) cc_final: 0.8669 (mmm) REVERT: p 116 TYR cc_start: 0.8749 (p90) cc_final: 0.8476 (p90) REVERT: p 130 GLU cc_start: 0.8598 (tp30) cc_final: 0.8383 (tp30) outliers start: 125 outliers final: 88 residues processed: 298 average time/residue: 0.1383 time to fit residues: 66.5992 Evaluate side-chains 289 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 189 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 LEU Chi-restraints excluded: chain 1 residue 42 ILE Chi-restraints excluded: chain 1 residue 53 LEU Chi-restraints excluded: chain 1 residue 57 ILE Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 112 THR Chi-restraints excluded: chain 1 residue 128 ILE Chi-restraints excluded: chain 1 residue 133 SER Chi-restraints excluded: chain 1 residue 150 LEU Chi-restraints excluded: chain 1 residue 155 ASP Chi-restraints excluded: chain 1 residue 168 ASP Chi-restraints excluded: chain 1 residue 185 GLN Chi-restraints excluded: chain 1 residue 189 VAL Chi-restraints excluded: chain 2 residue 33 SER Chi-restraints excluded: chain 2 residue 73 THR Chi-restraints excluded: chain 2 residue 95 LEU Chi-restraints excluded: chain 2 residue 127 GLN Chi-restraints excluded: chain 2 residue 136 ILE Chi-restraints excluded: chain 2 residue 142 SER Chi-restraints excluded: chain 2 residue 155 THR Chi-restraints excluded: chain 2 residue 176 THR Chi-restraints excluded: chain 3 residue 11 LYS Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 56 ASP Chi-restraints excluded: chain 3 residue 64 LYS Chi-restraints excluded: chain 3 residue 76 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 106 TYR Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 29 MET Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 9 GLN Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 80 MET Chi-restraints excluded: chain O residue 83 PHE Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 147 ASP Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 140 MET Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain n residue 95 VAL Chi-restraints excluded: chain n residue 130 LEU Chi-restraints excluded: chain n residue 141 THR Chi-restraints excluded: chain n residue 147 ILE Chi-restraints excluded: chain n residue 157 VAL Chi-restraints excluded: chain n residue 164 THR Chi-restraints excluded: chain o residue 15 SER Chi-restraints excluded: chain o residue 22 GLU Chi-restraints excluded: chain o residue 25 VAL Chi-restraints excluded: chain o residue 43 VAL Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain o residue 101 ILE Chi-restraints excluded: chain p residue 12 GLU Chi-restraints excluded: chain p residue 31 LEU Chi-restraints excluded: chain p residue 41 ILE Chi-restraints excluded: chain p residue 74 VAL Chi-restraints excluded: chain p residue 112 THR Chi-restraints excluded: chain p residue 138 VAL Chi-restraints excluded: chain p residue 175 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 40.0000 chunk 239 optimal weight: 6.9990 chunk 188 optimal weight: 20.0000 chunk 216 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 139 GLN ** o 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.163316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.102532 restraints weight = 45947.409| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.98 r_work: 0.3294 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20658 Z= 0.178 Angle : 0.574 8.907 27915 Z= 0.305 Chirality : 0.041 0.182 3132 Planarity : 0.003 0.032 3564 Dihedral : 4.778 58.598 2754 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.97 % Favored : 92.41 % Rotamer: Outliers : 5.49 % Allowed : 29.40 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.16), residues: 2568 helix: 1.21 (0.20), residues: 745 sheet: -0.84 (0.27), residues: 367 loop : -1.72 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 105 TYR 0.019 0.001 TYR 1 45 PHE 0.041 0.002 PHE N 166 TRP 0.040 0.002 TRP B 42 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00417 (20658) covalent geometry : angle 0.57430 (27915) hydrogen bonds : bond 0.04443 ( 695) hydrogen bonds : angle 4.52951 ( 1974) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 202 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: 1 29 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8612 (mtm) REVERT: 1 71 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7978 (mm) REVERT: 3 52 ARG cc_start: 0.7489 (mmm160) cc_final: 0.7285 (mmm160) REVERT: 3 58 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7976 (tp30) REVERT: 3 64 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7376 (mmtt) REVERT: 3 84 ASP cc_start: 0.8502 (m-30) cc_final: 0.8211 (m-30) REVERT: A 73 THR cc_start: 0.4912 (OUTLIER) cc_final: 0.4644 (t) REVERT: A 99 MET cc_start: 0.2187 (pmm) cc_final: 0.1624 (ptp) REVERT: A 118 TYR cc_start: 0.3681 (m-80) cc_final: 0.3293 (m-10) REVERT: A 131 LEU cc_start: 0.3439 (OUTLIER) cc_final: 0.3222 (mt) REVERT: A 177 ILE cc_start: 0.5133 (OUTLIER) cc_final: 0.4481 (mp) REVERT: B 81 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5766 (mp) REVERT: B 148 ARG cc_start: 0.4251 (ptt-90) cc_final: 0.3920 (pmt-80) REVERT: C 35 SER cc_start: 0.5663 (OUTLIER) cc_final: 0.5391 (p) REVERT: N 18 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.5918 (ttm-80) REVERT: N 186 MET cc_start: 0.6721 (mtt) cc_final: 0.6505 (mtm) REVERT: O 9 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8557 (pp30) REVERT: P 26 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7659 (pp20) REVERT: P 162 PHE cc_start: 0.8484 (t80) cc_final: 0.8204 (t80) REVERT: Q 140 MET cc_start: 0.0242 (ttm) cc_final: -0.0517 (ttm) REVERT: Q 147 ASP cc_start: 0.4124 (OUTLIER) cc_final: 0.3750 (m-30) REVERT: R 94 LYS cc_start: 0.1921 (mttm) cc_final: 0.1683 (tptp) REVERT: p 56 ASN cc_start: 0.8768 (t0) cc_final: 0.8466 (t0) REVERT: p 82 MET cc_start: 0.9061 (tpp) cc_final: 0.8631 (mmm) REVERT: p 130 GLU cc_start: 0.8564 (tp30) cc_final: 0.8353 (tp30) outliers start: 120 outliers final: 93 residues processed: 296 average time/residue: 0.1329 time to fit residues: 64.0597 Evaluate side-chains 295 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 190 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 LEU Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 42 ILE Chi-restraints excluded: chain 1 residue 53 LEU Chi-restraints excluded: chain 1 residue 57 ILE Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 112 THR Chi-restraints excluded: chain 1 residue 128 ILE Chi-restraints excluded: chain 1 residue 133 SER Chi-restraints excluded: chain 1 residue 150 LEU Chi-restraints excluded: chain 1 residue 155 ASP Chi-restraints excluded: chain 1 residue 168 ASP Chi-restraints excluded: chain 2 residue 33 SER Chi-restraints excluded: chain 2 residue 73 THR Chi-restraints excluded: chain 2 residue 95 LEU Chi-restraints excluded: chain 2 residue 104 SER Chi-restraints excluded: chain 2 residue 136 ILE Chi-restraints excluded: chain 2 residue 140 MET Chi-restraints excluded: chain 2 residue 142 SER Chi-restraints excluded: chain 2 residue 155 THR Chi-restraints excluded: chain 2 residue 176 THR Chi-restraints excluded: chain 3 residue 11 LYS Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 56 ASP Chi-restraints excluded: chain 3 residue 64 LYS Chi-restraints excluded: chain 3 residue 76 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 106 TYR Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 29 MET Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 9 GLN Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 80 MET Chi-restraints excluded: chain O residue 83 PHE Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 26 GLU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 147 ASP Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 140 MET Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain n residue 95 VAL Chi-restraints excluded: chain n residue 130 LEU Chi-restraints excluded: chain n residue 141 THR Chi-restraints excluded: chain n residue 147 ILE Chi-restraints excluded: chain n residue 157 VAL Chi-restraints excluded: chain n residue 164 THR Chi-restraints excluded: chain o residue 15 SER Chi-restraints excluded: chain o residue 22 GLU Chi-restraints excluded: chain o residue 43 VAL Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain o residue 101 ILE Chi-restraints excluded: chain p residue 12 GLU Chi-restraints excluded: chain p residue 31 LEU Chi-restraints excluded: chain p residue 41 ILE Chi-restraints excluded: chain p residue 74 VAL Chi-restraints excluded: chain p residue 99 MET Chi-restraints excluded: chain p residue 112 THR Chi-restraints excluded: chain p residue 136 ILE Chi-restraints excluded: chain p residue 138 VAL Chi-restraints excluded: chain p residue 175 VAL Chi-restraints excluded: chain p residue 177 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 166 optimal weight: 0.0570 chunk 209 optimal weight: 0.3980 chunk 147 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 234 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 181 optimal weight: 30.0000 chunk 244 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN C 139 GLN ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.164958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.104990 restraints weight = 46021.738| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.16 r_work: 0.3336 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20658 Z= 0.114 Angle : 0.542 9.325 27915 Z= 0.287 Chirality : 0.039 0.180 3132 Planarity : 0.003 0.033 3564 Dihedral : 4.507 55.283 2754 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.15 % Favored : 93.22 % Rotamer: Outliers : 4.39 % Allowed : 30.96 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.16), residues: 2568 helix: 1.46 (0.20), residues: 742 sheet: -0.75 (0.27), residues: 378 loop : -1.63 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 105 TYR 0.014 0.001 TYR 1 45 PHE 0.022 0.001 PHE N 175 TRP 0.042 0.002 TRP B 42 HIS 0.004 0.001 HIS 2 161 Details of bonding type rmsd covalent geometry : bond 0.00252 (20658) covalent geometry : angle 0.54246 (27915) hydrogen bonds : bond 0.03982 ( 695) hydrogen bonds : angle 4.31761 ( 1974) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 214 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 57 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8751 (mt) REVERT: 1 71 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8012 (mm) REVERT: 1 185 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8320 (mt0) REVERT: 2 17 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7701 (mt-10) REVERT: 3 58 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7770 (tp30) REVERT: 3 84 ASP cc_start: 0.8463 (m-30) cc_final: 0.8147 (m-30) REVERT: A 73 THR cc_start: 0.5093 (OUTLIER) cc_final: 0.4829 (t) REVERT: A 99 MET cc_start: 0.2053 (pmm) cc_final: 0.1374 (ptp) REVERT: A 118 TYR cc_start: 0.3669 (m-80) cc_final: 0.3396 (m-10) REVERT: A 177 ILE cc_start: 0.5128 (OUTLIER) cc_final: 0.4496 (mp) REVERT: B 81 LEU cc_start: 0.6251 (OUTLIER) cc_final: 0.5925 (mp) REVERT: C 24 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7508 (t70) REVERT: C 35 SER cc_start: 0.5795 (OUTLIER) cc_final: 0.5551 (p) REVERT: I 18 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7931 (tm-30) REVERT: N 186 MET cc_start: 0.6910 (mtt) cc_final: 0.6695 (mtm) REVERT: P 26 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7656 (pp20) REVERT: P 162 PHE cc_start: 0.8555 (t80) cc_final: 0.8298 (t80) REVERT: Q 140 MET cc_start: 0.0881 (ttm) cc_final: 0.0383 (ttp) REVERT: Q 147 ASP cc_start: 0.4095 (OUTLIER) cc_final: 0.3740 (m-30) REVERT: R 94 LYS cc_start: 0.2066 (mttm) cc_final: 0.1823 (tptp) REVERT: p 56 ASN cc_start: 0.8750 (t0) cc_final: 0.8440 (t0) REVERT: p 82 MET cc_start: 0.9011 (tpp) cc_final: 0.8636 (mmm) outliers start: 96 outliers final: 74 residues processed: 286 average time/residue: 0.1372 time to fit residues: 63.8308 Evaluate side-chains 284 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 200 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 LEU Chi-restraints excluded: chain 1 residue 42 ILE Chi-restraints excluded: chain 1 residue 53 LEU Chi-restraints excluded: chain 1 residue 57 ILE Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 133 SER Chi-restraints excluded: chain 1 residue 150 LEU Chi-restraints excluded: chain 1 residue 185 GLN Chi-restraints excluded: chain 1 residue 189 VAL Chi-restraints excluded: chain 2 residue 33 SER Chi-restraints excluded: chain 2 residue 73 THR Chi-restraints excluded: chain 2 residue 95 LEU Chi-restraints excluded: chain 2 residue 136 ILE Chi-restraints excluded: chain 2 residue 140 MET Chi-restraints excluded: chain 2 residue 144 THR Chi-restraints excluded: chain 2 residue 176 THR Chi-restraints excluded: chain 3 residue 11 LYS Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 56 ASP Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 65 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 106 TYR Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 80 MET Chi-restraints excluded: chain O residue 83 PHE Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 26 GLU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 147 ASP Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 140 MET Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain n residue 95 VAL Chi-restraints excluded: chain n residue 141 THR Chi-restraints excluded: chain o residue 15 SER Chi-restraints excluded: chain o residue 22 GLU Chi-restraints excluded: chain o residue 25 VAL Chi-restraints excluded: chain o residue 43 VAL Chi-restraints excluded: chain p residue 12 GLU Chi-restraints excluded: chain p residue 31 LEU Chi-restraints excluded: chain p residue 41 ILE Chi-restraints excluded: chain p residue 74 VAL Chi-restraints excluded: chain p residue 99 MET Chi-restraints excluded: chain p residue 112 THR Chi-restraints excluded: chain p residue 138 VAL Chi-restraints excluded: chain p residue 155 THR Chi-restraints excluded: chain p residue 175 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 170 optimal weight: 9.9990 chunk 246 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 130 optimal weight: 0.0870 chunk 88 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 118 optimal weight: 0.5980 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.165007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.105322 restraints weight = 45806.726| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.92 r_work: 0.3327 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20658 Z= 0.130 Angle : 0.555 9.336 27915 Z= 0.295 Chirality : 0.040 0.180 3132 Planarity : 0.003 0.051 3564 Dihedral : 4.447 55.030 2754 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.23 % Favored : 93.19 % Rotamer: Outliers : 4.44 % Allowed : 30.77 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.16), residues: 2568 helix: 1.50 (0.20), residues: 735 sheet: -0.76 (0.27), residues: 382 loop : -1.63 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 52 TYR 0.024 0.001 TYR C 118 PHE 0.051 0.001 PHE N 166 TRP 0.038 0.002 TRP B 42 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00298 (20658) covalent geometry : angle 0.55488 (27915) hydrogen bonds : bond 0.04016 ( 695) hydrogen bonds : angle 4.31892 ( 1974) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 204 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 57 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8707 (mt) REVERT: 1 71 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8000 (mm) REVERT: 1 185 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8232 (mt0) REVERT: 2 17 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7597 (mt-10) REVERT: 3 58 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7750 (tp30) REVERT: 3 84 ASP cc_start: 0.8306 (m-30) cc_final: 0.8018 (m-30) REVERT: A 73 THR cc_start: 0.5099 (OUTLIER) cc_final: 0.4835 (t) REVERT: A 118 TYR cc_start: 0.3749 (m-80) cc_final: 0.3356 (m-10) REVERT: A 177 ILE cc_start: 0.5098 (OUTLIER) cc_final: 0.4863 (mp) REVERT: B 81 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5703 (mp) REVERT: B 178 MET cc_start: 0.1178 (ptt) cc_final: 0.0647 (pmm) REVERT: C 35 SER cc_start: 0.5343 (OUTLIER) cc_final: 0.5056 (p) REVERT: O 38 GLN cc_start: 0.7548 (tm-30) cc_final: 0.7161 (tm-30) REVERT: P 26 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7430 (pp20) REVERT: P 162 PHE cc_start: 0.8379 (t80) cc_final: 0.8133 (t80) REVERT: Q 140 MET cc_start: 0.0588 (ttm) cc_final: 0.0113 (ttp) REVERT: Q 147 ASP cc_start: 0.4016 (OUTLIER) cc_final: 0.3615 (m-30) REVERT: p 56 ASN cc_start: 0.8669 (t0) cc_final: 0.8349 (t0) REVERT: p 82 MET cc_start: 0.8968 (tpp) cc_final: 0.8550 (mmm) outliers start: 97 outliers final: 77 residues processed: 279 average time/residue: 0.1387 time to fit residues: 62.5945 Evaluate side-chains 282 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 196 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 LEU Chi-restraints excluded: chain 1 residue 42 ILE Chi-restraints excluded: chain 1 residue 53 LEU Chi-restraints excluded: chain 1 residue 57 ILE Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 128 ILE Chi-restraints excluded: chain 1 residue 133 SER Chi-restraints excluded: chain 1 residue 150 LEU Chi-restraints excluded: chain 1 residue 185 GLN Chi-restraints excluded: chain 1 residue 189 VAL Chi-restraints excluded: chain 2 residue 33 SER Chi-restraints excluded: chain 2 residue 73 THR Chi-restraints excluded: chain 2 residue 74 VAL Chi-restraints excluded: chain 2 residue 95 LEU Chi-restraints excluded: chain 2 residue 140 MET Chi-restraints excluded: chain 2 residue 142 SER Chi-restraints excluded: chain 2 residue 144 THR Chi-restraints excluded: chain 2 residue 176 THR Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 80 MET Chi-restraints excluded: chain O residue 83 PHE Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 26 GLU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 147 ASP Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 140 MET Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain n residue 95 VAL Chi-restraints excluded: chain n residue 141 THR Chi-restraints excluded: chain o residue 15 SER Chi-restraints excluded: chain o residue 22 GLU Chi-restraints excluded: chain o residue 25 VAL Chi-restraints excluded: chain o residue 43 VAL Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain o residue 101 ILE Chi-restraints excluded: chain p residue 12 GLU Chi-restraints excluded: chain p residue 31 LEU Chi-restraints excluded: chain p residue 41 ILE Chi-restraints excluded: chain p residue 74 VAL Chi-restraints excluded: chain p residue 99 MET Chi-restraints excluded: chain p residue 112 THR Chi-restraints excluded: chain p residue 138 VAL Chi-restraints excluded: chain p residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 53 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 238 optimal weight: 0.0050 chunk 207 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 228 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.165360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.105646 restraints weight = 46108.517| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.06 r_work: 0.3341 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20658 Z= 0.125 Angle : 0.550 9.556 27915 Z= 0.292 Chirality : 0.039 0.182 3132 Planarity : 0.003 0.055 3564 Dihedral : 4.393 54.194 2754 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.15 % Favored : 93.26 % Rotamer: Outliers : 4.02 % Allowed : 31.00 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.16), residues: 2568 helix: 1.58 (0.20), residues: 736 sheet: -0.73 (0.27), residues: 382 loop : -1.59 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 105 TYR 0.018 0.001 TYR C 118 PHE 0.048 0.001 PHE N 166 TRP 0.036 0.002 TRP B 42 HIS 0.004 0.001 HIS 2 161 Details of bonding type rmsd covalent geometry : bond 0.00283 (20658) covalent geometry : angle 0.55008 (27915) hydrogen bonds : bond 0.03917 ( 695) hydrogen bonds : angle 4.25432 ( 1974) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 205 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 57 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8710 (mt) REVERT: 1 71 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8040 (mm) REVERT: 1 185 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8378 (mt0) REVERT: 2 17 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7620 (mt-10) REVERT: 3 58 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7788 (tp30) REVERT: 3 84 ASP cc_start: 0.8525 (m-30) cc_final: 0.8000 (t0) REVERT: A 118 TYR cc_start: 0.3545 (m-80) cc_final: 0.3206 (m-10) REVERT: B 178 MET cc_start: 0.1055 (ptt) cc_final: 0.0490 (pmm) REVERT: C 24 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7459 (t70) REVERT: C 35 SER cc_start: 0.5469 (OUTLIER) cc_final: 0.5176 (p) REVERT: I 18 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7731 (tm-30) REVERT: P 26 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7449 (pp20) REVERT: P 162 PHE cc_start: 0.8370 (t80) cc_final: 0.8144 (t80) REVERT: Q 147 ASP cc_start: 0.3895 (OUTLIER) cc_final: 0.3520 (m-30) REVERT: p 56 ASN cc_start: 0.8669 (t0) cc_final: 0.8337 (t0) REVERT: p 82 MET cc_start: 0.8991 (tpp) cc_final: 0.8599 (mmm) outliers start: 88 outliers final: 73 residues processed: 275 average time/residue: 0.1388 time to fit residues: 62.3447 Evaluate side-chains 272 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 192 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 LEU Chi-restraints excluded: chain 1 residue 42 ILE Chi-restraints excluded: chain 1 residue 53 LEU Chi-restraints excluded: chain 1 residue 57 ILE Chi-restraints excluded: chain 1 residue 71 LEU Chi-restraints excluded: chain 1 residue 128 ILE Chi-restraints excluded: chain 1 residue 133 SER Chi-restraints excluded: chain 1 residue 150 LEU Chi-restraints excluded: chain 1 residue 185 GLN Chi-restraints excluded: chain 1 residue 189 VAL Chi-restraints excluded: chain 2 residue 74 VAL Chi-restraints excluded: chain 2 residue 95 LEU Chi-restraints excluded: chain 2 residue 140 MET Chi-restraints excluded: chain 2 residue 142 SER Chi-restraints excluded: chain 2 residue 144 THR Chi-restraints excluded: chain 2 residue 176 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 80 MET Chi-restraints excluded: chain O residue 83 PHE Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain P residue 26 GLU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 147 ASP Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 140 MET Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain n residue 95 VAL Chi-restraints excluded: chain n residue 141 THR Chi-restraints excluded: chain o residue 15 SER Chi-restraints excluded: chain o residue 22 GLU Chi-restraints excluded: chain o residue 25 VAL Chi-restraints excluded: chain o residue 43 VAL Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain o residue 101 ILE Chi-restraints excluded: chain p residue 12 GLU Chi-restraints excluded: chain p residue 31 LEU Chi-restraints excluded: chain p residue 41 ILE Chi-restraints excluded: chain p residue 74 VAL Chi-restraints excluded: chain p residue 99 MET Chi-restraints excluded: chain p residue 112 THR Chi-restraints excluded: chain p residue 138 VAL Chi-restraints excluded: chain p residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 210 optimal weight: 10.0000 chunk 11 optimal weight: 0.4980 chunk 90 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 26 optimal weight: 0.0170 chunk 197 optimal weight: 50.0000 chunk 189 optimal weight: 10.0000 overall best weight: 2.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 13 GLN ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN P 161 HIS ** o 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.164711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.104550 restraints weight = 46134.778| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.10 r_work: 0.3329 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20658 Z= 0.140 Angle : 0.565 10.877 27915 Z= 0.299 Chirality : 0.040 0.184 3132 Planarity : 0.003 0.042 3564 Dihedral : 4.436 55.444 2754 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.58 % Favored : 92.83 % Rotamer: Outliers : 4.02 % Allowed : 30.86 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.16), residues: 2568 helix: 1.56 (0.20), residues: 739 sheet: -0.73 (0.27), residues: 380 loop : -1.59 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 18 TYR 0.018 0.001 TYR 1 45 PHE 0.054 0.002 PHE N 166 TRP 0.034 0.002 TRP B 42 HIS 0.004 0.001 HIS Q 13 Details of bonding type rmsd covalent geometry : bond 0.00325 (20658) covalent geometry : angle 0.56468 (27915) hydrogen bonds : bond 0.04004 ( 695) hydrogen bonds : angle 4.26803 ( 1974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10764.11 seconds wall clock time: 184 minutes 6.02 seconds (11046.02 seconds total)