Starting phenix.real_space_refine on Tue Jun 17 14:35:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j1l_61075/06_2025/9j1l_61075.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j1l_61075/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9j1l_61075/06_2025/9j1l_61075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j1l_61075/06_2025/9j1l_61075.map" model { file = "/net/cci-nas-00/data/ceres_data/9j1l_61075/06_2025/9j1l_61075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j1l_61075/06_2025/9j1l_61075.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.05, per 1000 atoms: 0.64 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: 4.98 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.03 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: 6.04 Time building geometry restraints manager: 5.95 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 47.240 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.840 ------------------------------------------------------------------------------- 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 : 17.79 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (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 TRP 0.042 0.002 TRP B 42 HIS 0.003 0.001 HIS Q 13 PHE 0.047 0.002 PHE N 166 TYR 0.030 0.001 TYR B 117 ARG 0.004 0.000 ARG p 173 Details of bonding type rmsd hydrogen bonds : bond 0.13862 ( 695) hydrogen bonds : angle 5.50184 ( 1974) covalent geometry : bond 0.00391 (20658) covalent geometry : angle 0.61211 (27915) *********************** 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 : 2.310 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: 0.2974 time to fit residues: 96.4009 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 : 2.299 ------------------------------------------------------------------------------- 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 212 optimal weight: 0.9990 chunk 191 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 65 optimal weight: 40.0000 chunk 128 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 197 optimal weight: 30.0000 chunk 76 optimal weight: 30.0000 chunk 120 optimal weight: 0.9980 chunk 147 optimal weight: 30.0000 chunk 228 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.163118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101275 restraints weight = 46163.835| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.26 r_work: 0.3271 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20658 Z= 0.254 Angle : 0.644 10.475 27915 Z= 0.344 Chirality : 0.043 0.179 3132 Planarity : 0.004 0.040 3564 Dihedral : 4.987 58.613 2758 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.55 % Favored : 91.86 % Rotamer: Outliers : 4.76 % Allowed : 28.26 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.16), residues: 2568 helix: 1.23 (0.20), residues: 730 sheet: -1.01 (0.26), residues: 390 loop : -1.61 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 42 HIS 0.007 0.001 HIS Q 13 PHE 0.032 0.002 PHE 1 17 TYR 0.023 0.002 TYR 1 45 ARG 0.004 0.001 ARG C 148 Details of bonding type rmsd hydrogen bonds : bond 0.05069 ( 695) hydrogen bonds : angle 4.89501 ( 1974) covalent geometry : bond 0.00597 (20658) covalent geometry : angle 0.64424 (27915) *********************** 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 302 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 198 time to evaluate : 2.294 Fit side-chains REVERT: 1 71 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8005 (mm) REVERT: A 99 MET cc_start: 0.2012 (pmm) cc_final: 0.1406 (ptp) REVERT: B 7 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8026 (mmt) REVERT: B 140 MET cc_start: 0.4931 (mpp) cc_final: 0.4279 (ttp) REVERT: B 148 ARG cc_start: 0.4128 (OUTLIER) cc_final: 0.3846 (pmt-80) REVERT: O 58 GLU cc_start: 0.9111 (tp30) cc_final: 0.8866 (tp30) REVERT: R 94 LYS cc_start: 0.1851 (mttm) cc_final: 0.1490 (tptt) REVERT: p 56 ASN cc_start: 0.8785 (t0) cc_final: 0.8583 (t0) outliers start: 104 outliers final: 57 residues processed: 282 average time/residue: 0.4013 time to fit residues: 178.9808 Evaluate side-chains 241 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 181 time to evaluate : 3.771 ------------------------------------------------------------------------------- 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 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 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 10 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 7 MET 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 I residue 4 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 161 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 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 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 141 THR Chi-restraints excluded: chain n residue 157 VAL Chi-restraints excluded: chain o residue 43 VAL Chi-restraints excluded: chain o residue 83 PHE Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain o residue 101 ILE Chi-restraints excluded: chain p residue 31 LEU Chi-restraints excluded: chain p residue 41 ILE Chi-restraints excluded: chain p residue 71 GLU 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 82 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 179 optimal weight: 30.0000 chunk 106 optimal weight: 20.0000 chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 47 optimal weight: 50.0000 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 127 GLN ** 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 = 0.4370 r_free = 0.4370 target = 0.163997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.103104 restraints weight = 45858.027| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.31 r_work: 0.3291 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1463 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= 0.176 Angle : 0.571 8.012 27915 Z= 0.305 Chirality : 0.041 0.155 3132 Planarity : 0.003 0.035 3564 Dihedral : 4.748 57.586 2754 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.43 % Favored : 92.99 % Rotamer: Outliers : 4.12 % Allowed : 28.81 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.16), residues: 2568 helix: 1.27 (0.20), residues: 734 sheet: -0.95 (0.26), residues: 385 loop : -1.65 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 42 HIS 0.005 0.001 HIS Q 13 PHE 0.038 0.002 PHE N 166 TYR 0.018 0.001 TYR 1 45 ARG 0.004 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.04597 ( 695) hydrogen bonds : angle 4.62868 ( 1974) covalent geometry : bond 0.00412 (20658) covalent geometry : angle 0.57087 (27915) *********************** 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: 90 poor density : 190 time to evaluate : 2.370 Fit side-chains REVERT: 1 71 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7985 (mm) REVERT: 1 147 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8623 (mt) REVERT: A 99 MET cc_start: 0.1800 (pmm) cc_final: 0.1197 (ptp) REVERT: B 140 MET cc_start: 0.4664 (mpp) cc_final: 0.4143 (ttp) REVERT: B 148 ARG cc_start: 0.4086 (OUTLIER) cc_final: 0.3781 (pmt-80) REVERT: B 178 MET cc_start: 0.3370 (pmm) cc_final: 0.3072 (ptt) REVERT: I 7 MET cc_start: 0.8506 (mtp) cc_final: 0.8087 (mtp) REVERT: O 58 GLU cc_start: 0.9136 (tp30) cc_final: 0.8914 (tp30) REVERT: P 162 PHE cc_start: 0.8389 (t80) cc_final: 0.8125 (t80) REVERT: R 94 LYS cc_start: 0.1776 (mttm) cc_final: 0.1509 (tptt) REVERT: p 56 ASN cc_start: 0.8672 (t0) cc_final: 0.8398 (t0) REVERT: p 145 TYR cc_start: 0.8080 (t80) cc_final: 0.7673 (t80) outliers start: 90 outliers final: 52 residues processed: 260 average time/residue: 0.2722 time to fit residues: 115.4987 Evaluate side-chains 237 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 182 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 MET 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 147 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 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 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 69 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 161 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 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 11 ASN Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain Q residue 5 VAL 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 n residue 60 VAL Chi-restraints excluded: chain n residue 83 ASP Chi-restraints excluded: chain n residue 147 ILE 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 p residue 31 LEU 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 72 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 64 optimal weight: 30.0000 chunk 16 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 178 optimal weight: 30.0000 chunk 171 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.163766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.102717 restraints weight = 46118.624| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.16 r_work: 0.3296 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20658 Z= 0.178 Angle : 0.563 8.280 27915 Z= 0.301 Chirality : 0.040 0.185 3132 Planarity : 0.003 0.031 3564 Dihedral : 4.721 57.924 2754 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.17 % Favored : 92.25 % Rotamer: Outliers : 5.26 % Allowed : 28.58 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.16), residues: 2568 helix: 1.29 (0.20), residues: 739 sheet: -0.86 (0.27), residues: 371 loop : -1.68 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 42 HIS 0.005 0.001 HIS A 161 PHE 0.041 0.002 PHE N 166 TYR 0.020 0.001 TYR 1 45 ARG 0.004 0.000 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.04487 ( 695) hydrogen bonds : angle 4.55630 ( 1974) covalent geometry : bond 0.00417 (20658) covalent geometry : angle 0.56336 (27915) *********************** 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 311 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 196 time to evaluate : 2.477 Fit side-chains revert: symmetry clash REVERT: 1 71 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8028 (mm) REVERT: 1 185 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: A 99 MET cc_start: 0.1860 (pmm) cc_final: 0.1228 (ptp) REVERT: B 7 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8037 (mmt) REVERT: B 140 MET cc_start: 0.4537 (mpp) cc_final: 0.3913 (ttp) REVERT: B 148 ARG cc_start: 0.4202 (ptt-90) cc_final: 0.3896 (pmt-80) REVERT: B 178 MET cc_start: 0.3276 (pmm) cc_final: 0.3037 (ptt) REVERT: C 24 HIS cc_start: 0.8147 (OUTLIER) cc_final: 0.7444 (t70) REVERT: I 7 MET cc_start: 0.8667 (mtp) cc_final: 0.8304 (mtp) REVERT: O 9 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8580 (pp30) REVERT: P 162 PHE cc_start: 0.8514 (t80) cc_final: 0.8226 (t80) REVERT: R 94 LYS cc_start: 0.1830 (mttm) cc_final: 0.1573 (tptt) REVERT: p 56 ASN cc_start: 0.8763 (t0) cc_final: 0.8485 (t0) REVERT: p 114 GLN cc_start: 0.7255 (mt0) cc_final: 0.6961 (mt0) REVERT: p 145 TYR cc_start: 0.8067 (t80) cc_final: 0.7755 (t80) outliers start: 115 outliers final: 77 residues processed: 288 average time/residue: 0.2879 time to fit residues: 134.7387 Evaluate side-chains 266 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 184 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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 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 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 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 7 MET Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 147 ASP 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 172 LEU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 161 THR 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 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 16 LEU 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 136 ILE 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 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 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 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 138 VAL 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 107 optimal weight: 30.0000 chunk 209 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 141 optimal weight: 0.0010 chunk 1 optimal weight: 7.9990 chunk 65 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 48 optimal weight: 40.0000 chunk 54 optimal weight: 8.9990 chunk 245 optimal weight: 0.9980 overall best weight: 4.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 174 GLN I 13 HIS ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 GLN P 174 GLN ** o 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.162436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.101375 restraints weight = 46301.232| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.00 r_work: 0.3270 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 20658 Z= 0.242 Angle : 0.618 8.245 27915 Z= 0.329 Chirality : 0.042 0.163 3132 Planarity : 0.003 0.038 3564 Dihedral : 4.901 57.910 2754 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.59 % Favored : 91.78 % Rotamer: Outliers : 6.45 % Allowed : 28.17 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.16), residues: 2568 helix: 1.14 (0.20), residues: 739 sheet: -1.01 (0.26), residues: 390 loop : -1.77 (0.15), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 42 HIS 0.007 0.001 HIS A 161 PHE 0.039 0.002 PHE N 166 TYR 0.022 0.002 TYR 1 45 ARG 0.004 0.001 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 695) hydrogen bonds : angle 4.69365 ( 1974) covalent geometry : bond 0.00572 (20658) covalent geometry : angle 0.61783 (27915) *********************** 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 330 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 189 time to evaluate : 3.665 Fit side-chains REVERT: 1 71 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8000 (mm) REVERT: 1 185 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8282 (mt0) REVERT: 3 52 ARG cc_start: 0.7553 (mmm160) cc_final: 0.7256 (mmm160) REVERT: 3 58 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7785 (tp30) REVERT: 3 84 ASP cc_start: 0.8428 (m-30) cc_final: 0.8196 (m-30) REVERT: A 99 MET cc_start: 0.2099 (pmm) cc_final: 0.1569 (ptp) REVERT: B 7 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.7926 (mmt) REVERT: B 140 MET cc_start: 0.4520 (mpp) cc_final: 0.4014 (ttp) REVERT: B 148 ARG cc_start: 0.4222 (OUTLIER) cc_final: 0.3915 (pmt-80) REVERT: B 178 MET cc_start: 0.3308 (pmm) cc_final: 0.3053 (ptt) REVERT: C 24 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7415 (t70) REVERT: C 86 GLN cc_start: 0.3051 (OUTLIER) cc_final: 0.2754 (mp10) REVERT: I 7 MET cc_start: 0.8690 (mtp) cc_final: 0.8347 (mtp) REVERT: I 131 LEU cc_start: 0.1468 (OUTLIER) cc_final: 0.1009 (tp) REVERT: N 18 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6286 (ttm-80) REVERT: O 83 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7719 (p90) REVERT: P 12 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7815 (pm20) REVERT: Q 63 LYS cc_start: 0.2232 (OUTLIER) cc_final: 0.1800 (mtmt) REVERT: R 94 LYS cc_start: 0.1757 (mttm) cc_final: 0.1468 (tptt) REVERT: p 56 ASN cc_start: 0.8780 (t0) cc_final: 0.8476 (t0) REVERT: p 116 TYR cc_start: 0.8765 (p90) cc_final: 0.8478 (p90) REVERT: p 145 TYR cc_start: 0.8104 (t80) cc_final: 0.7763 (t80) outliers start: 141 outliers final: 94 residues processed: 305 average time/residue: 0.3490 time to fit residues: 172.2083 Evaluate side-chains 290 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 185 time to evaluate : 2.632 ------------------------------------------------------------------------------- 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 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 185 GLN Chi-restraints excluded: chain 2 residue 33 SER 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 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 7 MET Chi-restraints excluded: chain B residue 15 THR 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 151 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 17 GLU 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 86 GLN 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 131 LEU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 161 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 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 11 ASN Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 23 THR 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 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 96 LEU 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 88 ILE Chi-restraints excluded: chain o residue 101 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 148 optimal weight: 30.0000 chunk 185 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 149 optimal weight: 0.4980 chunk 194 optimal weight: 8.9990 chunk 178 optimal weight: 30.0000 chunk 116 optimal weight: 30.0000 chunk 41 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 38 GLN R 139 GLN ** o 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 102 ASN p 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.164634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.104212 restraints weight = 46240.647| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.16 r_work: 0.3321 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2063 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= 0.127 Angle : 0.540 8.747 27915 Z= 0.288 Chirality : 0.039 0.168 3132 Planarity : 0.003 0.033 3564 Dihedral : 4.608 57.051 2754 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.62 % Favored : 92.76 % Rotamer: Outliers : 4.66 % Allowed : 29.86 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2568 helix: 1.43 (0.20), residues: 732 sheet: -0.82 (0.27), residues: 370 loop : -1.64 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 42 HIS 0.004 0.001 HIS 2 161 PHE 0.020 0.001 PHE N 175 TYR 0.015 0.001 TYR 1 45 ARG 0.005 0.000 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 695) hydrogen bonds : angle 4.41383 ( 1974) covalent geometry : bond 0.00284 (20658) covalent geometry : angle 0.53996 (27915) *********************** 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 304 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 202 time to evaluate : 3.804 Fit side-chains REVERT: 1 57 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8648 (mt) REVERT: 1 71 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8069 (mm) REVERT: 1 185 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: 2 12 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8369 (pm20) REVERT: 3 31 LEU cc_start: 0.8514 (tp) cc_final: 0.8250 (tp) REVERT: 3 52 ARG cc_start: 0.7543 (mmm160) cc_final: 0.7343 (mmm160) REVERT: 3 58 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7805 (tp30) REVERT: 3 84 ASP cc_start: 0.8475 (m-30) cc_final: 0.8211 (m-30) REVERT: A 99 MET cc_start: 0.2027 (pmm) cc_final: 0.1360 (ptp) REVERT: A 118 TYR cc_start: 0.3657 (m-80) cc_final: 0.3383 (m-10) REVERT: B 140 MET cc_start: 0.4295 (mpp) cc_final: 0.4002 (ttp) REVERT: B 148 ARG cc_start: 0.4259 (OUTLIER) cc_final: 0.3955 (pmt-80) REVERT: B 178 MET cc_start: 0.3199 (pmm) cc_final: 0.2685 (ptt) REVERT: C 86 GLN cc_start: 0.2976 (OUTLIER) cc_final: 0.2701 (mp10) REVERT: N 18 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.6003 (ttm-80) REVERT: O 9 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8634 (pp30) REVERT: P 162 PHE cc_start: 0.8550 (t80) cc_final: 0.8278 (t80) REVERT: R 94 LYS cc_start: 0.1959 (mttm) cc_final: 0.1713 (tptt) REVERT: p 56 ASN cc_start: 0.8788 (t0) cc_final: 0.8491 (t0) REVERT: p 82 MET cc_start: 0.9051 (tpp) cc_final: 0.8664 (mmm) REVERT: p 130 GLU cc_start: 0.8608 (tp30) cc_final: 0.8400 (tp30) REVERT: p 145 TYR cc_start: 0.8016 (t80) cc_final: 0.7734 (t80) outliers start: 102 outliers final: 69 residues processed: 279 average time/residue: 0.4408 time to fit residues: 206.9467 Evaluate side-chains 270 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 193 time to evaluate : 7.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 150 LEU Chi-restraints excluded: chain 1 residue 161 THR Chi-restraints excluded: chain 1 residue 185 GLN Chi-restraints excluded: chain 2 residue 12 GLU 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 142 SER 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 54 LEU 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 115 ASP Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 151 LEU 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 86 GLN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 161 THR 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 36 SER 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 140 MET Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 48 THR 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 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 31 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 133 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 222 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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 38 GLN ** 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 = 0.4356 r_free = 0.4356 target = 0.162880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.101953 restraints weight = 46228.707| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.13 r_work: 0.3287 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20658 Z= 0.198 Angle : 0.593 8.652 27915 Z= 0.315 Chirality : 0.041 0.193 3132 Planarity : 0.003 0.032 3564 Dihedral : 4.771 58.392 2754 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.32 % Favored : 92.06 % Rotamer: Outliers : 5.26 % Allowed : 29.49 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.16), residues: 2568 helix: 1.34 (0.20), residues: 730 sheet: -0.92 (0.27), residues: 373 loop : -1.65 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 42 HIS 0.006 0.001 HIS A 161 PHE 0.047 0.002 PHE N 166 TYR 0.021 0.002 TYR 1 45 ARG 0.008 0.001 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 695) hydrogen bonds : angle 4.56597 ( 1974) covalent geometry : bond 0.00466 (20658) covalent geometry : angle 0.59280 (27915) *********************** 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 308 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 193 time to evaluate : 2.802 Fit side-chains revert: symmetry clash REVERT: 1 71 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8011 (mm) REVERT: 1 185 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8295 (mt0) REVERT: 2 12 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: 3 52 ARG cc_start: 0.7445 (mmm160) cc_final: 0.7215 (mmm160) REVERT: 3 58 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7830 (tp30) REVERT: 3 84 ASP cc_start: 0.8475 (m-30) cc_final: 0.8196 (m-30) REVERT: A 99 MET cc_start: 0.2060 (pmm) cc_final: 0.1394 (ptp) REVERT: B 148 ARG cc_start: 0.4231 (OUTLIER) cc_final: 0.3921 (pmt-80) REVERT: B 178 MET cc_start: 0.3186 (pmm) cc_final: 0.2753 (ptt) REVERT: C 24 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7469 (t70) REVERT: C 86 GLN cc_start: 0.3668 (OUTLIER) cc_final: 0.3416 (mp10) REVERT: N 18 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.6073 (ttm-80) REVERT: P 12 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7904 (pm20) REVERT: Q 63 LYS cc_start: 0.2445 (OUTLIER) cc_final: 0.2070 (mtmt) REVERT: R 94 LYS cc_start: 0.1994 (mttm) cc_final: 0.1736 (tptp) REVERT: p 56 ASN cc_start: 0.8778 (t0) cc_final: 0.8466 (t0) REVERT: p 82 MET cc_start: 0.9052 (tpp) cc_final: 0.8610 (mmm) REVERT: p 145 TYR cc_start: 0.8067 (t80) cc_final: 0.7713 (t80) outliers start: 115 outliers final: 91 residues processed: 285 average time/residue: 0.4057 time to fit residues: 188.1564 Evaluate side-chains 286 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 186 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 12 GLU 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 127 GLN 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 144 THR Chi-restraints excluded: chain 2 residue 155 THR Chi-restraints excluded: chain 2 residue 176 THR Chi-restraints excluded: chain 3 residue 54 LEU 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 159 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 15 THR 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 151 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 17 GLU 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 86 GLN 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 112 THR Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 161 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 9 GLU Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 23 THR 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 8 SER 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 63 LYS 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 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 138 VAL Chi-restraints excluded: chain p residue 155 THR Chi-restraints excluded: chain p residue 175 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 70 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 chunk 226 optimal weight: 8.9990 chunk 188 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 197 optimal weight: 0.4980 chunk 208 optimal weight: 3.9990 chunk 232 optimal weight: 0.0870 chunk 245 optimal weight: 5.9990 chunk 153 optimal weight: 0.4980 overall best weight: 1.6162 ------------------------------------------------------------------------------- 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 38 GLN P 161 HIS ** 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 = 0.4378 r_free = 0.4378 target = 0.164632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.104568 restraints weight = 46468.480| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.03 r_work: 0.3332 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20658 Z= 0.121 Angle : 0.543 9.301 27915 Z= 0.288 Chirality : 0.039 0.174 3132 Planarity : 0.003 0.033 3564 Dihedral : 4.507 56.396 2754 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.19 % Favored : 93.19 % Rotamer: Outliers : 4.85 % Allowed : 29.72 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 2568 helix: 1.51 (0.20), residues: 734 sheet: -0.77 (0.27), residues: 371 loop : -1.58 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 42 HIS 0.004 0.001 HIS 2 161 PHE 0.046 0.001 PHE N 166 TYR 0.015 0.001 TYR 1 45 ARG 0.004 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 695) hydrogen bonds : angle 4.32832 ( 1974) covalent geometry : bond 0.00272 (20658) covalent geometry : angle 0.54278 (27915) *********************** 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 309 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 203 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 57 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8674 (mt) REVERT: 1 71 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8022 (mm) REVERT: 1 185 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8197 (mt0) REVERT: 2 12 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: 2 17 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7646 (mt-10) REVERT: 2 172 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8124 (tp) REVERT: 3 58 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7826 (tp30) REVERT: 3 84 ASP cc_start: 0.8377 (m-30) cc_final: 0.8082 (m-30) REVERT: A 118 TYR cc_start: 0.3728 (m-80) cc_final: 0.3407 (m-10) REVERT: A 130 GLU cc_start: 0.2058 (OUTLIER) cc_final: 0.1511 (tp30) REVERT: A 177 ILE cc_start: 0.5132 (OUTLIER) cc_final: 0.4824 (mp) REVERT: B 178 MET cc_start: 0.3012 (pmm) cc_final: 0.2709 (ptt) REVERT: C 24 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7438 (t70) REVERT: C 35 SER cc_start: 0.5872 (OUTLIER) cc_final: 0.5633 (p) REVERT: I 18 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7804 (tm-30) REVERT: N 18 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.6066 (mtm-85) REVERT: N 29 MET cc_start: 0.8459 (mtm) cc_final: 0.8190 (mtp) REVERT: P 12 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7690 (pm20) REVERT: P 162 PHE cc_start: 0.8302 (t80) cc_final: 0.7976 (t80) REVERT: P 163 ASP cc_start: 0.7938 (m-30) cc_final: 0.7488 (m-30) REVERT: R 94 LYS cc_start: 0.1737 (mttm) cc_final: 0.1537 (tptp) REVERT: p 56 ASN cc_start: 0.8706 (t0) cc_final: 0.8379 (t0) REVERT: p 82 MET cc_start: 0.8970 (tpp) cc_final: 0.8576 (mmm) REVERT: p 145 TYR cc_start: 0.8019 (t80) cc_final: 0.7626 (t80) outliers start: 106 outliers final: 80 residues processed: 288 average time/residue: 0.2950 time to fit residues: 136.3409 Evaluate side-chains 281 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 190 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 12 GLU 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 127 GLN 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 144 THR Chi-restraints excluded: chain 2 residue 155 THR Chi-restraints excluded: chain 2 residue 172 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 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 130 GLU 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 151 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 17 GLU 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 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 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 9 GLU Chi-restraints excluded: chain P residue 12 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 8 SER 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 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 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 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 235 optimal weight: 10.0000 chunk 225 optimal weight: 4.9990 chunk 194 optimal weight: 30.0000 chunk 193 optimal weight: 0.9980 chunk 234 optimal weight: 50.0000 chunk 130 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 107 optimal weight: 40.0000 chunk 38 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** P 18 GLN ** 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 = 0.4362 r_free = 0.4362 target = 0.163334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.102790 restraints weight = 46156.572| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.07 r_work: 0.3297 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20658 Z= 0.185 Angle : 0.585 9.424 27915 Z= 0.311 Chirality : 0.041 0.181 3132 Planarity : 0.003 0.046 3564 Dihedral : 4.652 58.399 2754 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.13 % Favored : 92.25 % Rotamer: Outliers : 4.71 % Allowed : 30.13 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.16), residues: 2568 helix: 1.46 (0.20), residues: 729 sheet: -0.90 (0.27), residues: 373 loop : -1.61 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 42 HIS 0.005 0.001 HIS A 161 PHE 0.052 0.002 PHE N 166 TYR 0.020 0.001 TYR 1 45 ARG 0.009 0.001 ARG 3 52 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 695) hydrogen bonds : angle 4.49367 ( 1974) covalent geometry : bond 0.00436 (20658) covalent geometry : angle 0.58532 (27915) *********************** 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 296 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 193 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 71 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8016 (mm) REVERT: 1 185 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8201 (mt0) REVERT: 3 58 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7933 (tp30) REVERT: 3 61 HIS cc_start: 0.8122 (m-70) cc_final: 0.7894 (m90) REVERT: 3 84 ASP cc_start: 0.8441 (m-30) cc_final: 0.8114 (m-30) REVERT: A 118 TYR cc_start: 0.3599 (m-80) cc_final: 0.3249 (m-10) REVERT: A 130 GLU cc_start: 0.2135 (OUTLIER) cc_final: 0.1916 (tp30) REVERT: A 177 ILE cc_start: 0.4970 (OUTLIER) cc_final: 0.4684 (mp) REVERT: B 178 MET cc_start: 0.3078 (pmm) cc_final: 0.2830 (ptt) REVERT: C 24 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7470 (t70) REVERT: C 35 SER cc_start: 0.5636 (OUTLIER) cc_final: 0.5355 (p) REVERT: P 12 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7681 (pm20) REVERT: P 162 PHE cc_start: 0.8341 (t80) cc_final: 0.8066 (t80) REVERT: R 94 LYS cc_start: 0.1905 (mttm) cc_final: 0.1703 (tptp) REVERT: p 56 ASN cc_start: 0.8694 (t0) cc_final: 0.8372 (t0) REVERT: p 82 MET cc_start: 0.8986 (tpp) cc_final: 0.8561 (mmm) REVERT: p 145 TYR cc_start: 0.8074 (t80) cc_final: 0.7715 (t80) outliers start: 103 outliers final: 84 residues processed: 274 average time/residue: 0.2869 time to fit residues: 127.8460 Evaluate side-chains 276 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 185 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 127 GLN 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 144 THR Chi-restraints excluded: chain 2 residue 155 THR 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 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 130 GLU 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 151 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 17 GLU 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 112 THR Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 161 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 9 GLU Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 23 THR 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 23 THR Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain R residue 10 LYS 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 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 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 75 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 47 optimal weight: 40.0000 chunk 217 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 178 optimal weight: 40.0000 chunk 216 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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** ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** o 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.165754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.106151 restraints weight = 46376.728| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.18 r_work: 0.3355 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20658 Z= 0.111 Angle : 0.547 9.666 27915 Z= 0.288 Chirality : 0.039 0.185 3132 Planarity : 0.003 0.037 3564 Dihedral : 4.384 54.173 2754 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.58 % Allowed : 5.84 % Favored : 93.57 % Rotamer: Outliers : 3.25 % Allowed : 31.50 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.16), residues: 2568 helix: 1.56 (0.20), residues: 741 sheet: -0.83 (0.27), residues: 378 loop : -1.54 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 42 HIS 0.004 0.001 HIS 2 161 PHE 0.050 0.001 PHE N 166 TYR 0.016 0.001 TYR C 118 ARG 0.006 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 695) hydrogen bonds : angle 4.28553 ( 1974) covalent geometry : bond 0.00244 (20658) covalent geometry : angle 0.54703 (27915) ********************** 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 280 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 209 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 57 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8696 (mt) REVERT: 1 71 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7968 (mm) REVERT: 2 17 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7606 (mt-10) REVERT: 3 58 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7827 (tp30) REVERT: 3 84 ASP cc_start: 0.8515 (m-30) cc_final: 0.8023 (t0) REVERT: A 118 TYR cc_start: 0.3897 (m-80) cc_final: 0.3561 (m-10) REVERT: A 177 ILE cc_start: 0.4776 (OUTLIER) cc_final: 0.4359 (mt) REVERT: B 178 MET cc_start: 0.3044 (pmm) cc_final: 0.2809 (ptt) REVERT: C 35 SER cc_start: 0.5677 (OUTLIER) cc_final: 0.5352 (p) REVERT: I 18 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7795 (tt0) REVERT: P 162 PHE cc_start: 0.8493 (t80) cc_final: 0.8254 (t80) REVERT: R 94 LYS cc_start: 0.1885 (mttm) cc_final: 0.1683 (tptp) REVERT: p 56 ASN cc_start: 0.8760 (t0) cc_final: 0.8443 (t0) REVERT: p 82 MET cc_start: 0.9034 (tpp) cc_final: 0.8707 (mmm) REVERT: p 145 TYR cc_start: 0.8063 (t80) cc_final: 0.7670 (t80) outliers start: 71 outliers final: 58 residues processed: 263 average time/residue: 0.2772 time to fit residues: 117.1410 Evaluate side-chains 257 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 195 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 128 ILE Chi-restraints excluded: chain 1 residue 133 SER Chi-restraints excluded: chain 1 residue 150 LEU 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 127 GLN Chi-restraints excluded: chain 2 residue 136 ILE Chi-restraints excluded: chain 2 residue 142 SER Chi-restraints excluded: chain 2 residue 176 THR 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 159 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 151 LEU 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 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 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 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 Q residue 8 SER Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 31 LEU 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 164 THR Chi-restraints excluded: chain o residue 22 GLU Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain p residue 31 LEU 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 20 optimal weight: 0.9980 chunk 178 optimal weight: 40.0000 chunk 6 optimal weight: 6.9990 chunk 96 optimal weight: 0.3980 chunk 228 optimal weight: 20.0000 chunk 151 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 227 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 147 optimal weight: 40.0000 overall best weight: 3.0784 ------------------------------------------------------------------------------- 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 ** 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 = 0.4371 r_free = 0.4371 target = 0.163973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.103809 restraints weight = 46089.544| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.00 r_work: 0.3314 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2694 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= 0.168 Angle : 0.583 9.779 27915 Z= 0.308 Chirality : 0.040 0.181 3132 Planarity : 0.003 0.068 3564 Dihedral : 4.533 58.137 2754 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.78 % Favored : 92.60 % Rotamer: Outliers : 3.66 % Allowed : 31.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2568 helix: 1.52 (0.20), residues: 733 sheet: -0.81 (0.27), residues: 382 loop : -1.59 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 42 HIS 0.005 0.001 HIS A 161 PHE 0.053 0.002 PHE N 166 TYR 0.020 0.001 TYR 1 45 ARG 0.007 0.001 ARG O 52 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 695) hydrogen bonds : angle 4.40751 ( 1974) covalent geometry : bond 0.00393 (20658) covalent geometry : angle 0.58322 (27915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21331.55 seconds wall clock time: 378 minutes 6.80 seconds (22686.80 seconds total)