Starting phenix.real_space_refine on Mon Aug 25 13:21:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jgi_61465/08_2025/9jgi_61465.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jgi_61465/08_2025/9jgi_61465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jgi_61465/08_2025/9jgi_61465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jgi_61465/08_2025/9jgi_61465.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jgi_61465/08_2025/9jgi_61465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jgi_61465/08_2025/9jgi_61465.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 17675 2.51 5 N 4467 2.21 5 O 5596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27798 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1906 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "B" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1906 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "C" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1906 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "D" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1906 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "E" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1906 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "F" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1906 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "G" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1759 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 1 Chain: "H" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1906 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "I" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1728 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 Chain: "J" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1906 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "K" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1759 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 1 Chain: "L" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1906 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "M" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1742 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 1 Chain: "N" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1906 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "O" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1750 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 1 Time building chain proxies: 7.59, per 1000 atoms: 0.27 Number of scatterers: 27798 At special positions: 0 Unit cell: (132.8, 132.8, 157.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 5596 8.00 N 4467 7.00 C 17675 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: 2.94 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6696 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 38 sheets defined 2.7% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'C' and resid 69 through 77 removed outlier: 4.408A pdb=" N LEU C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 77 removed outlier: 3.899A pdb=" N THR D 76 " --> pdb=" O TRP D 72 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 72 through 77' Processing helix chain 'E' and resid 44 through 48 removed outlier: 4.247A pdb=" N LYS E 48 " --> pdb=" O ILE E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 74 removed outlier: 3.858A pdb=" N LEU E 73 " --> pdb=" O ASP E 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 74 removed outlier: 3.654A pdb=" N LEU F 73 " --> pdb=" O ASP F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 75 removed outlier: 3.671A pdb=" N LEU G 73 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 77 removed outlier: 3.877A pdb=" N LEU H 73 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR H 76 " --> pdb=" O TRP H 72 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 77 removed outlier: 3.868A pdb=" N THR I 76 " --> pdb=" O TRP I 72 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN I 77 " --> pdb=" O LEU I 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 72 through 77' Processing helix chain 'J' and resid 69 through 77 removed outlier: 4.129A pdb=" N LEU J 73 " --> pdb=" O ASP J 69 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR J 76 " --> pdb=" O TRP J 72 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN J 77 " --> pdb=" O LEU J 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 77 removed outlier: 3.735A pdb=" N LEU K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR K 76 " --> pdb=" O TRP K 72 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN K 77 " --> pdb=" O LEU K 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 78 removed outlier: 4.033A pdb=" N LEU L 73 " --> pdb=" O ASP L 69 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR L 76 " --> pdb=" O TRP L 72 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN L 77 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 74 removed outlier: 3.933A pdb=" N LEU O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 4 through 5 current: chain 'A' and resid 21 through 25 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 21 through 25 current: chain 'A' and resid 48 through 64 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 48 through 64 current: chain 'A' and resid 187 through 200 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 217 through 222 current: chain 'C' and resid 148 through 159 Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 97 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 85 through 97 current: chain 'A' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 123 through 126 current: chain 'B' and resid 232 through 236 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 209 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 207 through 209 current: chain 'B' and resid 21 through 22 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 21 through 22 current: chain 'B' and resid 58 through 65 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 65 current: chain 'B' and resid 187 through 200 Processing sheet with id=AA5, first strand: chain 'B' and resid 40 through 43 removed outlier: 3.956A pdb=" N LEU B 41 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 43 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 48 " --> pdb=" O GLY B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 82 through 97 current: chain 'B' and resid 146 through 162 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 146 through 162 current: chain 'E' and resid 187 through 192 Processing sheet with id=AA7, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.914A pdb=" N ALA E 30 " --> pdb=" O LEU B 208 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 27 through 33 current: chain 'E' and resid 52 through 65 removed outlier: 4.422A pdb=" N ILE E 59 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 15 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 21 through 24 current: chain 'C' and resid 57 through 65 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 65 current: chain 'C' and resid 187 through 201 removed outlier: 4.641A pdb=" N LYS C 219 " --> pdb=" O SER C 201 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 217 through 222 current: chain 'D' and resid 124 through 126 Processing sheet with id=AA9, first strand: chain 'C' and resid 41 through 42 removed outlier: 6.532A pdb=" N LEU C 41 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 105 removed outlier: 4.012A pdb=" N VAL C 104 " --> pdb=" O TYR C 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 15 removed outlier: 3.652A pdb=" N VAL D 11 " --> pdb=" O THR D 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 24 current: chain 'D' and resid 52 through 65 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 52 through 65 current: chain 'D' and resid 190 through 199 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 217 through 222 current: chain 'E' and resid 124 through 125 Processing sheet with id=AB3, first strand: chain 'D' and resid 103 through 105 Processing sheet with id=AB4, first strand: chain 'E' and resid 103 through 105 Processing sheet with id=AB5, first strand: chain 'E' and resid 171 through 173 removed outlier: 5.974A pdb=" N TYR E 171 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN E 197 " --> pdb=" O TYR E 171 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL E 173 " --> pdb=" O PHE E 195 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 15 removed outlier: 3.663A pdb=" N VAL F 11 " --> pdb=" O THR F 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 21 through 24 current: chain 'F' and resid 49 through 64 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 49 through 64 current: chain 'F' and resid 187 through 199 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 217 through 222 current: chain 'J' and resid 124 through 126 Processing sheet with id=AB7, first strand: chain 'F' and resid 85 through 97 removed outlier: 3.958A pdb=" N GLY F 95 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU F 147 " --> pdb=" O GLY F 95 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 103 through 105 Processing sheet with id=AB9, first strand: chain 'F' and resid 160 through 162 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 160 through 162 current: chain 'H' and resid 53 through 65 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 53 through 65 current: chain 'H' and resid 187 through 200 Processing sheet with id=AC1, first strand: chain 'G' and resid 4 through 5 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 4 through 5 current: chain 'G' and resid 21 through 24 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 21 through 24 current: chain 'G' and resid 58 through 64 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 58 through 64 current: chain 'G' and resid 187 through 200 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 217 through 222 current: chain 'K' and resid 160 through 161 Processing sheet with id=AC2, first strand: chain 'G' and resid 82 through 97 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 82 through 97 current: chain 'G' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 123 through 126 current: chain 'I' and resid 22 through 23 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 22 through 23 current: chain 'I' and resid 60 through 65 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 60 through 65 current: chain 'I' and resid 187 through 200 Processing sheet with id=AC3, first strand: chain 'G' and resid 103 through 105 Processing sheet with id=AC4, first strand: chain 'H' and resid 85 through 89 Processing sheet with id=AC5, first strand: chain 'H' and resid 92 through 93 Processing sheet with id=AC6, first strand: chain 'H' and resid 160 through 162 removed outlier: 3.775A pdb=" N ALA N 232 " --> pdb=" O ILE H 162 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER N 189 " --> pdb=" O ALA N 179 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 204 through 208 removed outlier: 3.529A pdb=" N GLN N 34 " --> pdb=" O PHE H 204 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS N 64 " --> pdb=" O GLN N 28 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA N 30 " --> pdb=" O THR N 62 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR N 62 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE N 32 " --> pdb=" O ASN N 60 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN N 60 " --> pdb=" O PHE N 32 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN N 34 " --> pdb=" O GLU N 58 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU N 58 " --> pdb=" O GLN N 34 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE N 36 " --> pdb=" O GLU N 56 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU N 56 " --> pdb=" O ILE N 36 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU N 38 " --> pdb=" O LYS N 54 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LYS N 54 " --> pdb=" O GLU N 38 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS N 40 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ILE N 52 " --> pdb=" O LYS N 40 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE N 59 " --> pdb=" O ALA N 222 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 85 through 92 removed outlier: 4.025A pdb=" N GLY I 157 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS I 155 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR I 148 " --> pdb=" O TYR I 117 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE I 126 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE I 116 " --> pdb=" O TYR I 124 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR I 124 " --> pdb=" O PHE I 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 160 through 162 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 160 through 162 current: chain 'O' and resid 58 through 64 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 58 through 64 current: chain 'O' and resid 187 through 200 Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 15 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 21 through 24 current: chain 'J' and resid 51 through 64 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 51 through 64 current: chain 'J' and resid 187 through 201 removed outlier: 4.826A pdb=" N LYS J 219 " --> pdb=" O SER J 201 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 217 through 222 current: chain 'L' and resid 123 through 126 Processing sheet with id=AD2, first strand: chain 'J' and resid 103 through 105 Processing sheet with id=AD3, first strand: chain 'K' and resid 11 through 15 removed outlier: 3.768A pdb=" N VAL K 11 " --> pdb=" O THR K 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 21 through 24 current: chain 'K' and resid 58 through 64 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 58 through 64 current: chain 'K' and resid 187 through 200 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 217 through 222 current: chain 'M' and resid 123 through 126 Processing sheet with id=AD4, first strand: chain 'K' and resid 85 through 97 removed outlier: 4.774A pdb=" N GLY K 95 " --> pdb=" O LEU K 147 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU K 147 " --> pdb=" O GLY K 95 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL K 114 " --> pdb=" O ILE K 126 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 103 through 105 Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 15 removed outlier: 3.510A pdb=" N VAL L 11 " --> pdb=" O THR L 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 21 through 24 current: chain 'L' and resid 56 through 65 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 56 through 65 current: chain 'L' and resid 187 through 201 removed outlier: 4.767A pdb=" N LYS L 219 " --> pdb=" O SER L 201 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 217 through 222 current: chain 'N' and resid 125 through 126 Processing sheet with id=AD7, first strand: chain 'L' and resid 40 through 43 removed outlier: 6.699A pdb=" N LEU L 41 " --> pdb=" O LEU L 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY L 43 " --> pdb=" O LYS L 48 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS L 48 " --> pdb=" O GLY L 43 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 12 through 15 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 12 through 15 current: chain 'M' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 59 through 65 current: chain 'M' and resid 187 through 200 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 217 through 222 current: chain 'O' and resid 123 through 126 Processing sheet with id=AD9, first strand: chain 'M' and resid 103 through 104 removed outlier: 3.522A pdb=" N VAL M 104 " --> pdb=" O TYR M 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 103 through 105 Processing sheet with id=AE2, first strand: chain 'O' and resid 103 through 105 183 hydrogen bonds defined for protein. 504 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: 2.71 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5113 1.32 - 1.44: 6838 1.44 - 1.57: 16189 1.57 - 1.69: 3 1.69 - 1.81: 120 Bond restraints: 28263 Sorted by residual: bond pdb=" CA SER E 207 " pdb=" CB SER E 207 " ideal model delta sigma weight residual 1.525 1.455 0.070 1.29e-02 6.01e+03 2.96e+01 bond pdb=" CA SER E 199 " pdb=" CB SER E 199 " ideal model delta sigma weight residual 1.530 1.472 0.058 1.58e-02 4.01e+03 1.34e+01 bond pdb=" N VAL C 128 " pdb=" CA VAL C 128 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.15e-02 7.56e+03 1.22e+01 bond pdb=" N VAL B 173 " pdb=" CA VAL B 173 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.20e-02 6.94e+03 1.03e+01 bond pdb=" N VAL N 198 " pdb=" CA VAL N 198 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.15e-02 7.56e+03 9.17e+00 ... (remaining 28258 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 37420 2.24 - 4.49: 641 4.49 - 6.73: 104 6.73 - 8.98: 15 8.98 - 11.22: 8 Bond angle restraints: 38188 Sorted by residual: angle pdb=" CA PHE B 195 " pdb=" CB PHE B 195 " pdb=" CG PHE B 195 " ideal model delta sigma weight residual 113.80 123.27 -9.47 1.00e+00 1.00e+00 8.97e+01 angle pdb=" C ASN N 197 " pdb=" CA ASN N 197 " pdb=" CB ASN N 197 " ideal model delta sigma weight residual 111.42 101.36 10.06 1.31e+00 5.83e-01 5.90e+01 angle pdb=" C PHE N 195 " pdb=" CA PHE N 195 " pdb=" CB PHE N 195 " ideal model delta sigma weight residual 109.08 118.16 -9.08 1.49e+00 4.50e-01 3.71e+01 angle pdb=" CA PHE C 140 " pdb=" CB PHE C 140 " pdb=" CG PHE C 140 " ideal model delta sigma weight residual 113.80 119.86 -6.06 1.00e+00 1.00e+00 3.67e+01 angle pdb=" N GLN E 194 " pdb=" CA GLN E 194 " pdb=" CB GLN E 194 " ideal model delta sigma weight residual 109.97 102.03 7.94 1.47e+00 4.63e-01 2.92e+01 ... (remaining 38183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14259 17.99 - 35.99: 2117 35.99 - 53.98: 644 53.98 - 71.98: 143 71.98 - 89.97: 55 Dihedral angle restraints: 17218 sinusoidal: 6869 harmonic: 10349 Sorted by residual: dihedral pdb=" CA PRO M 196 " pdb=" C PRO M 196 " pdb=" N ASN M 197 " pdb=" CA ASN M 197 " ideal model delta harmonic sigma weight residual 180.00 -152.65 -27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA VAL O 22 " pdb=" C VAL O 22 " pdb=" N PHE O 23 " pdb=" CA PHE O 23 " ideal model delta harmonic sigma weight residual 180.00 154.57 25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA TYR N 151 " pdb=" C TYR N 151 " pdb=" N GLN N 152 " pdb=" CA GLN N 152 " ideal model delta harmonic sigma weight residual 180.00 154.63 25.37 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 17215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3698 0.066 - 0.132: 623 0.132 - 0.198: 37 0.198 - 0.264: 8 0.264 - 0.330: 5 Chirality restraints: 4371 Sorted by residual: chirality pdb=" CA ASN E 197 " pdb=" N ASN E 197 " pdb=" C ASN E 197 " pdb=" CB ASN E 197 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILE C 235 " pdb=" CA ILE C 235 " pdb=" CG1 ILE C 235 " pdb=" CG2 ILE C 235 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CG LEU H 50 " pdb=" CB LEU H 50 " pdb=" CD1 LEU H 50 " pdb=" CD2 LEU H 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 4368 not shown) Planarity restraints: 4899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 197 " 0.023 2.00e-02 2.50e+03 4.78e-02 2.29e+01 pdb=" C ASN E 197 " -0.083 2.00e-02 2.50e+03 pdb=" O ASN E 197 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL E 198 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS H 48 " -0.055 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO H 49 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO H 49 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO H 49 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 2 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C LYS B 2 " 0.056 2.00e-02 2.50e+03 pdb=" O LYS B 2 " -0.021 2.00e-02 2.50e+03 pdb=" N THR B 3 " -0.019 2.00e-02 2.50e+03 ... (remaining 4896 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 317 2.62 - 3.19: 22767 3.19 - 3.76: 39661 3.76 - 4.33: 54847 4.33 - 4.90: 92216 Nonbonded interactions: 209808 Sorted by model distance: nonbonded pdb=" OG1 THR M 62 " pdb=" OE2 GLU M 217 " model vdw 2.046 3.040 nonbonded pdb=" OD1 ASP F 18 " pdb=" N GLY F 19 " model vdw 2.056 3.120 nonbonded pdb=" NE ARG H 15 " pdb=" OE2 GLU H 169 " model vdw 2.074 3.120 nonbonded pdb=" OE2 GLU K 205 " pdb=" OG SER K 207 " model vdw 2.093 3.040 nonbonded pdb=" O GLY H 43 " pdb=" OH TYR H 51 " model vdw 2.093 3.040 ... (remaining 209803 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 33 or resid 57 through 241)) selection = (chain 'B' and (resid 1 through 33 or resid 57 through 241)) selection = (chain 'C' and (resid 1 through 33 or resid 57 through 241)) selection = (chain 'D' and (resid 1 through 33 or resid 57 through 241)) selection = (chain 'E' and (resid 1 through 33 or resid 57 through 241)) selection = (chain 'F' and (resid 1 through 33 or resid 57 through 241)) selection = (chain 'G' and (resid 1 through 33 or resid 57 through 241)) selection = (chain 'H' and (resid 1 through 33 or resid 57 through 241)) selection = chain 'I' selection = (chain 'J' and (resid 1 through 33 or resid 57 through 241)) selection = (chain 'K' and (resid 1 through 33 or resid 57 through 241)) selection = (chain 'L' and (resid 1 through 33 or resid 57 through 241)) selection = (chain 'M' and (resid 1 through 33 or resid 57 through 241)) selection = (chain 'N' and (resid 1 through 33 or resid 57 through 241)) selection = (chain 'O' and (resid 1 through 33 or resid 57 through 241)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 24.050 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 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 0.120 28263 Z= 0.219 Angle : 0.738 11.225 38188 Z= 0.431 Chirality : 0.048 0.330 4371 Planarity : 0.004 0.085 4899 Dihedral : 19.413 89.970 10522 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.44 % Favored : 90.27 % Rotamer: Outliers : 0.96 % Allowed : 38.59 % Favored : 60.45 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.14), residues: 3473 helix: -3.57 (0.45), residues: 82 sheet: -0.05 (0.14), residues: 1569 loop : -2.59 (0.13), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 15 TYR 0.022 0.001 TYR H 171 PHE 0.047 0.002 PHE K 220 TRP 0.011 0.001 TRP A 72 HIS 0.008 0.001 HIS I 94 Details of bonding type rmsd covalent geometry : bond 0.00424 (28263) covalent geometry : angle 0.73834 (38188) hydrogen bonds : bond 0.19257 ( 183) hydrogen bonds : angle 7.46348 ( 504) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 833 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: E 24 THR cc_start: 0.7672 (t) cc_final: 0.7402 (t) REVERT: E 197 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7356 (t0) REVERT: E 210 ASN cc_start: 0.8178 (t0) cc_final: 0.7722 (t0) REVERT: F 64 LYS cc_start: 0.7729 (ttmm) cc_final: 0.7423 (ttmm) outliers start: 29 outliers final: 16 residues processed: 845 average time/residue: 0.1680 time to fit residues: 220.5367 Evaluate side-chains 843 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 826 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 63 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 197 optimal weight: 0.0870 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0370 chunk 155 optimal weight: 0.0570 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN F 28 GLN M 94 HIS ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.141463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119541 restraints weight = 38641.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123753 restraints weight = 18132.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.126522 restraints weight = 10531.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.128376 restraints weight = 7127.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.129348 restraints weight = 5372.767| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 28263 Z= 0.096 Angle : 0.522 6.503 38188 Z= 0.281 Chirality : 0.044 0.208 4371 Planarity : 0.003 0.080 4899 Dihedral : 5.541 63.093 3809 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.15 % Favored : 91.59 % Rotamer: Outliers : 3.68 % Allowed : 35.31 % Favored : 61.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.14), residues: 3473 helix: -3.10 (0.48), residues: 82 sheet: 0.03 (0.14), residues: 1536 loop : -2.48 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 15 TYR 0.018 0.001 TYR C 51 PHE 0.013 0.001 PHE A 23 TRP 0.005 0.001 TRP M 72 HIS 0.007 0.001 HIS I 94 Details of bonding type rmsd covalent geometry : bond 0.00222 (28263) covalent geometry : angle 0.52234 (38188) hydrogen bonds : bond 0.02787 ( 183) hydrogen bonds : angle 5.38650 ( 504) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 836 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 217 GLU cc_start: 0.7032 (pm20) cc_final: 0.6814 (pm20) REVERT: B 235 ILE cc_start: 0.8289 (mt) cc_final: 0.8004 (mp) REVERT: C 26 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6344 (tm-30) REVERT: C 53 LEU cc_start: 0.8141 (tp) cc_final: 0.7908 (mt) REVERT: C 54 LYS cc_start: 0.7860 (mttp) cc_final: 0.7544 (mttp) REVERT: C 146 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8601 (mmmt) REVERT: C 185 GLU cc_start: 0.5643 (OUTLIER) cc_final: 0.5040 (mp0) REVERT: C 217 GLU cc_start: 0.6916 (tp30) cc_final: 0.6651 (tp30) REVERT: D 83 GLU cc_start: 0.8380 (mp0) cc_final: 0.8091 (mp0) REVERT: E 210 ASN cc_start: 0.8289 (t0) cc_final: 0.7838 (t0) REVERT: E 229 ASP cc_start: 0.7462 (m-30) cc_final: 0.7185 (m-30) REVERT: F 209 GLU cc_start: 0.6994 (mp0) cc_final: 0.6606 (mp0) REVERT: G 71 GLU cc_start: 0.7385 (mp0) cc_final: 0.6808 (mp0) REVERT: H 40 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7933 (mmtt) REVERT: H 209 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7003 (mm-30) REVERT: J 6 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: J 26 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6343 (tm-30) REVERT: J 207 SER cc_start: 0.8327 (t) cc_final: 0.7980 (p) REVERT: K 120 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7898 (mtmm) REVERT: L 64 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7644 (ttpp) REVERT: L 203 GLU cc_start: 0.7146 (tp30) cc_final: 0.6705 (mp0) REVERT: L 204 PHE cc_start: 0.6222 (t80) cc_final: 0.5999 (t80) REVERT: L 219 LYS cc_start: 0.8625 (mttt) cc_final: 0.8414 (mttm) REVERT: L 233 VAL cc_start: 0.8512 (m) cc_final: 0.8160 (p) REVERT: N 40 LYS cc_start: 0.7785 (mttp) cc_final: 0.6824 (mmtt) outliers start: 111 outliers final: 62 residues processed: 899 average time/residue: 0.1695 time to fit residues: 238.5924 Evaluate side-chains 886 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 821 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 117 TYR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 152 GLN Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 198 VAL Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 120 LYS Chi-restraints excluded: chain K residue 148 THR Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 167 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 203 GLU Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 151 TYR Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 201 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 0.0670 chunk 340 optimal weight: 0.5980 chunk 287 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 282 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118372 restraints weight = 38728.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.122617 restraints weight = 18239.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125384 restraints weight = 10639.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.127029 restraints weight = 7208.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128331 restraints weight = 5558.017| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28263 Z= 0.112 Angle : 0.516 7.981 38188 Z= 0.275 Chirality : 0.043 0.205 4371 Planarity : 0.003 0.067 4899 Dihedral : 5.026 46.697 3783 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.23 % Favored : 91.51 % Rotamer: Outliers : 4.70 % Allowed : 35.01 % Favored : 60.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.14), residues: 3473 helix: -2.64 (0.52), residues: 82 sheet: 0.02 (0.14), residues: 1578 loop : -2.41 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 15 TYR 0.021 0.001 TYR C 51 PHE 0.017 0.001 PHE L 204 TRP 0.008 0.001 TRP M 72 HIS 0.005 0.001 HIS I 94 Details of bonding type rmsd covalent geometry : bond 0.00266 (28263) covalent geometry : angle 0.51598 (38188) hydrogen bonds : bond 0.02976 ( 183) hydrogen bonds : angle 5.06135 ( 504) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 837 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4320 (OUTLIER) cc_final: 0.3557 (tm-30) REVERT: A 79 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6964 (tm-30) REVERT: B 69 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.5984 (m-30) REVERT: B 217 GLU cc_start: 0.6996 (pm20) cc_final: 0.6745 (pm20) REVERT: B 235 ILE cc_start: 0.8299 (mt) cc_final: 0.7966 (mp) REVERT: C 26 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6533 (tm-30) REVERT: C 53 LEU cc_start: 0.8113 (tp) cc_final: 0.7663 (tt) REVERT: C 146 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8525 (mmmt) REVERT: C 185 GLU cc_start: 0.5704 (OUTLIER) cc_final: 0.4943 (mp0) REVERT: D 54 LYS cc_start: 0.7916 (mmmt) cc_final: 0.7561 (mmmt) REVERT: E 26 GLU cc_start: 0.6750 (tp30) cc_final: 0.6360 (tp30) REVERT: E 198 VAL cc_start: 0.8162 (p) cc_final: 0.7922 (t) REVERT: E 210 ASN cc_start: 0.8303 (t0) cc_final: 0.7902 (t0) REVERT: E 229 ASP cc_start: 0.7469 (m-30) cc_final: 0.7188 (m-30) REVERT: F 64 LYS cc_start: 0.8046 (ttmm) cc_final: 0.7651 (ttmm) REVERT: F 84 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6656 (tm-30) REVERT: G 71 GLU cc_start: 0.7419 (mp0) cc_final: 0.6824 (mp0) REVERT: G 197 ASN cc_start: 0.7329 (t0) cc_final: 0.7055 (t0) REVERT: G 205 GLU cc_start: 0.6572 (tm-30) cc_final: 0.6344 (tm-30) REVERT: H 209 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6930 (mm-30) REVERT: I 239 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6700 (mmt-90) REVERT: J 6 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7569 (pt0) REVERT: J 26 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6372 (tm-30) REVERT: J 56 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5830 (tm-30) REVERT: J 207 SER cc_start: 0.8321 (t) cc_final: 0.7945 (p) REVERT: K 33 SER cc_start: 0.8620 (m) cc_final: 0.8234 (t) REVERT: L 64 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7656 (ttpp) REVERT: N 124 TYR cc_start: 0.8435 (t80) cc_final: 0.7933 (t80) outliers start: 142 outliers final: 86 residues processed: 916 average time/residue: 0.1716 time to fit residues: 246.6072 Evaluate side-chains 920 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 826 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 117 TYR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 152 GLN Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 163 LYS Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 239 ARG Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 218 ILE Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 167 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 203 GLU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 151 TYR Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 201 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 4 optimal weight: 0.0170 chunk 112 optimal weight: 0.0870 chunk 282 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 114 optimal weight: 0.0870 chunk 262 optimal weight: 0.7980 chunk 341 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 28 GLN E 77 GLN E 181 ASN ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 GLN O 77 GLN ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.141231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119142 restraints weight = 38621.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123400 restraints weight = 18200.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126195 restraints weight = 10658.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.127938 restraints weight = 7227.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128946 restraints weight = 5491.490| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 28263 Z= 0.089 Angle : 0.489 7.661 38188 Z= 0.260 Chirality : 0.043 0.202 4371 Planarity : 0.003 0.054 4899 Dihedral : 4.760 46.395 3780 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.43 % Favored : 92.31 % Rotamer: Outliers : 4.54 % Allowed : 35.21 % Favored : 60.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.14), residues: 3473 helix: -2.18 (0.56), residues: 76 sheet: 0.10 (0.14), residues: 1580 loop : -2.34 (0.13), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 15 TYR 0.017 0.001 TYR C 51 PHE 0.013 0.001 PHE L 204 TRP 0.005 0.001 TRP I 72 HIS 0.003 0.001 HIS I 94 Details of bonding type rmsd covalent geometry : bond 0.00208 (28263) covalent geometry : angle 0.48923 (38188) hydrogen bonds : bond 0.02492 ( 183) hydrogen bonds : angle 4.82450 ( 504) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 812 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4227 (OUTLIER) cc_final: 0.3937 (tt0) REVERT: A 79 GLU cc_start: 0.7311 (tm-30) cc_final: 0.7007 (tm-30) REVERT: B 69 ASP cc_start: 0.6579 (OUTLIER) cc_final: 0.6004 (m-30) REVERT: B 187 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8315 (t) REVERT: B 217 GLU cc_start: 0.7024 (pm20) cc_final: 0.6774 (pm20) REVERT: B 235 ILE cc_start: 0.8282 (mt) cc_final: 0.7970 (mp) REVERT: C 26 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6513 (tm-30) REVERT: C 53 LEU cc_start: 0.8094 (tp) cc_final: 0.7737 (tt) REVERT: C 54 LYS cc_start: 0.7788 (mttp) cc_final: 0.7524 (mttm) REVERT: C 146 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8627 (mmmt) REVERT: C 185 GLU cc_start: 0.5721 (OUTLIER) cc_final: 0.5050 (mp0) REVERT: D 14 LYS cc_start: 0.7919 (tptt) cc_final: 0.7679 (tptp) REVERT: D 54 LYS cc_start: 0.7899 (mmmt) cc_final: 0.7470 (mmmt) REVERT: E 77 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: E 198 VAL cc_start: 0.8240 (p) cc_final: 0.7986 (t) REVERT: E 205 GLU cc_start: 0.6829 (tm-30) cc_final: 0.6412 (tm-30) REVERT: E 210 ASN cc_start: 0.8297 (t0) cc_final: 0.7903 (t0) REVERT: F 103 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6380 (tppp) REVERT: G 26 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7341 (mm-30) REVERT: G 71 GLU cc_start: 0.7437 (mp0) cc_final: 0.6838 (mp0) REVERT: G 83 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7324 (mt-10) REVERT: G 205 GLU cc_start: 0.6565 (tm-30) cc_final: 0.6295 (tm-30) REVERT: H 88 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7481 (tttm) REVERT: I 109 LYS cc_start: 0.8306 (mmtt) cc_final: 0.8095 (mmtt) REVERT: J 6 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7540 (pt0) REVERT: J 26 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: J 56 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5901 (tm-30) REVERT: J 79 GLU cc_start: 0.7388 (tp30) cc_final: 0.7115 (tp30) REVERT: J 92 ARG cc_start: 0.8318 (ptp90) cc_final: 0.7971 (ptt-90) REVERT: J 207 SER cc_start: 0.8311 (t) cc_final: 0.7949 (p) REVERT: K 33 SER cc_start: 0.8645 (m) cc_final: 0.8283 (t) REVERT: L 2 LYS cc_start: 0.8066 (mmtm) cc_final: 0.7851 (mmtm) REVERT: L 64 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7666 (ttpp) REVERT: M 156 VAL cc_start: 0.8365 (m) cc_final: 0.8096 (m) REVERT: N 209 GLU cc_start: 0.6208 (pp20) cc_final: 0.5758 (pp20) REVERT: O 241 GLU cc_start: 0.6716 (pp20) cc_final: 0.6323 (pp20) outliers start: 137 outliers final: 78 residues processed: 890 average time/residue: 0.1666 time to fit residues: 232.8579 Evaluate side-chains 893 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 803 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 117 TYR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 152 GLN Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 93 GLU Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 167 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 151 TYR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 201 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 141 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 312 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 343 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 344 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN E 34 GLN ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 GLN M 94 HIS ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.138178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116068 restraints weight = 38617.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120372 restraints weight = 17897.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123094 restraints weight = 10361.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124940 restraints weight = 7031.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125886 restraints weight = 5279.125| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28263 Z= 0.150 Angle : 0.536 7.722 38188 Z= 0.285 Chirality : 0.044 0.200 4371 Planarity : 0.003 0.055 4899 Dihedral : 5.022 48.140 3779 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.04 % Favored : 90.70 % Rotamer: Outliers : 5.96 % Allowed : 34.28 % Favored : 59.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.14), residues: 3473 helix: -2.22 (0.55), residues: 82 sheet: 0.03 (0.14), residues: 1586 loop : -2.37 (0.13), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 15 TYR 0.026 0.001 TYR C 51 PHE 0.021 0.002 PHE H 195 TRP 0.010 0.001 TRP M 72 HIS 0.004 0.001 HIS I 94 Details of bonding type rmsd covalent geometry : bond 0.00359 (28263) covalent geometry : angle 0.53620 (38188) hydrogen bonds : bond 0.03027 ( 183) hydrogen bonds : angle 4.91683 ( 504) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 845 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4385 (OUTLIER) cc_final: 0.3694 (tp30) REVERT: A 79 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7037 (tm-30) REVERT: A 125 LYS cc_start: 0.8236 (ttpp) cc_final: 0.7928 (ttmp) REVERT: B 69 ASP cc_start: 0.6564 (OUTLIER) cc_final: 0.6005 (m-30) REVERT: B 84 GLU cc_start: 0.6922 (mp0) cc_final: 0.6536 (mp0) REVERT: B 187 VAL cc_start: 0.8513 (m) cc_final: 0.8281 (m) REVERT: B 217 GLU cc_start: 0.6990 (pm20) cc_final: 0.6727 (pm20) REVERT: B 235 ILE cc_start: 0.8220 (mt) cc_final: 0.7905 (mp) REVERT: C 146 LYS cc_start: 0.9042 (mmmt) cc_final: 0.8536 (mmmt) REVERT: C 184 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.7530 (m) REVERT: C 185 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.4781 (mp0) REVERT: D 54 LYS cc_start: 0.7916 (mmmt) cc_final: 0.7527 (mmmt) REVERT: D 135 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7858 (p) REVERT: E 26 GLU cc_start: 0.6743 (tp30) cc_final: 0.6337 (tp30) REVERT: E 185 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6538 (mp0) REVERT: E 198 VAL cc_start: 0.8304 (p) cc_final: 0.8070 (t) REVERT: E 205 GLU cc_start: 0.6896 (tm-30) cc_final: 0.6382 (tm-30) REVERT: E 210 ASN cc_start: 0.8317 (t0) cc_final: 0.7901 (t0) REVERT: E 236 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6901 (mt-10) REVERT: F 84 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6666 (tm-30) REVERT: F 103 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6371 (tppp) REVERT: G 21 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7279 (tm) REVERT: G 26 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7318 (mm-30) REVERT: G 71 GLU cc_start: 0.7410 (mp0) cc_final: 0.6859 (mp0) REVERT: G 83 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: G 86 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7904 (mtpp) REVERT: G 91 ASP cc_start: 0.8113 (t0) cc_final: 0.7767 (t0) REVERT: G 197 ASN cc_start: 0.7427 (t0) cc_final: 0.7132 (t0) REVERT: G 205 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6340 (tm-30) REVERT: H 186 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6614 (mp0) REVERT: H 209 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6908 (mm-30) REVERT: I 109 LYS cc_start: 0.8355 (mmtt) cc_final: 0.8115 (mmtt) REVERT: J 6 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: J 26 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6408 (tm-30) REVERT: J 73 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7990 (tt) REVERT: J 79 GLU cc_start: 0.7466 (tp30) cc_final: 0.7179 (tp30) REVERT: K 33 SER cc_start: 0.8654 (m) cc_final: 0.8274 (t) REVERT: K 82 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7634 (pm20) REVERT: K 109 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7925 (mptp) REVERT: K 220 PHE cc_start: 0.8391 (m-10) cc_final: 0.8184 (m-10) REVERT: L 64 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7662 (ttpp) REVERT: M 119 LYS cc_start: 0.8328 (ttmm) cc_final: 0.7948 (ttmm) REVERT: M 156 VAL cc_start: 0.8387 (m) cc_final: 0.8128 (m) REVERT: M 172 GLU cc_start: 0.6805 (mp0) cc_final: 0.6120 (mp0) REVERT: N 11 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7390 (t) REVERT: O 217 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5964 (tp30) outliers start: 180 outliers final: 116 residues processed: 948 average time/residue: 0.1711 time to fit residues: 254.8528 Evaluate side-chains 967 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 831 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 117 TYR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 226 THR Chi-restraints excluded: chain J residue 240 ASP Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 32 PHE Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 167 PHE Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 94 HIS Chi-restraints excluded: chain M residue 203 GLU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 15 ARG Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 151 TYR Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 217 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 129 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 69 optimal weight: 0.0050 chunk 134 optimal weight: 1.9990 chunk 200 optimal weight: 0.3980 chunk 330 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN E 28 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN N 34 GLN ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.117687 restraints weight = 38563.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121926 restraints weight = 18030.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.124720 restraints weight = 10478.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126382 restraints weight = 7082.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.127411 restraints weight = 5423.028| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28263 Z= 0.108 Angle : 0.514 8.175 38188 Z= 0.272 Chirality : 0.043 0.198 4371 Planarity : 0.003 0.055 4899 Dihedral : 4.896 51.008 3779 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.75 % Favored : 92.00 % Rotamer: Outliers : 5.10 % Allowed : 35.64 % Favored : 59.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.14), residues: 3473 helix: -2.15 (0.55), residues: 82 sheet: 0.00 (0.14), residues: 1589 loop : -2.31 (0.13), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 15 TYR 0.020 0.001 TYR C 51 PHE 0.012 0.001 PHE F 195 TRP 0.004 0.001 TRP I 72 HIS 0.009 0.001 HIS M 94 Details of bonding type rmsd covalent geometry : bond 0.00254 (28263) covalent geometry : angle 0.51440 (38188) hydrogen bonds : bond 0.02614 ( 183) hydrogen bonds : angle 4.83036 ( 504) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 815 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4432 (OUTLIER) cc_final: 0.3861 (tt0) REVERT: A 79 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7039 (tm-30) REVERT: A 125 LYS cc_start: 0.8228 (ttpp) cc_final: 0.7945 (tttp) REVERT: B 69 ASP cc_start: 0.6568 (OUTLIER) cc_final: 0.5989 (m-30) REVERT: B 84 GLU cc_start: 0.6900 (mp0) cc_final: 0.6470 (mp0) REVERT: B 217 GLU cc_start: 0.6969 (pm20) cc_final: 0.6734 (pm20) REVERT: B 235 ILE cc_start: 0.8248 (mt) cc_final: 0.7950 (mp) REVERT: C 53 LEU cc_start: 0.8163 (tp) cc_final: 0.7753 (tt) REVERT: C 146 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8531 (mmmt) REVERT: C 185 GLU cc_start: 0.5590 (OUTLIER) cc_final: 0.4660 (mp0) REVERT: D 54 LYS cc_start: 0.7890 (mmmt) cc_final: 0.7476 (mmmt) REVERT: D 135 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7796 (p) REVERT: E 26 GLU cc_start: 0.6684 (tp30) cc_final: 0.6341 (tp30) REVERT: E 198 VAL cc_start: 0.8307 (p) cc_final: 0.8085 (t) REVERT: E 205 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6421 (tm-30) REVERT: E 210 ASN cc_start: 0.8306 (t0) cc_final: 0.7897 (t0) REVERT: E 223 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8357 (mp) REVERT: E 236 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6843 (mt-10) REVERT: F 103 LYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6387 (tppp) REVERT: G 21 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7276 (tm) REVERT: G 26 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7314 (mm-30) REVERT: G 64 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7450 (mtpp) REVERT: G 71 GLU cc_start: 0.7352 (mp0) cc_final: 0.6826 (mp0) REVERT: G 83 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: G 86 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7789 (mtpp) REVERT: G 163 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7887 (mmtp) REVERT: G 197 ASN cc_start: 0.7358 (t0) cc_final: 0.7081 (t0) REVERT: G 205 GLU cc_start: 0.6578 (tm-30) cc_final: 0.6316 (tm-30) REVERT: H 88 LYS cc_start: 0.8094 (tmtt) cc_final: 0.7619 (tmtt) REVERT: H 209 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6958 (mm-30) REVERT: I 109 LYS cc_start: 0.8339 (mmtt) cc_final: 0.8080 (mmtt) REVERT: J 6 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7602 (pt0) REVERT: J 26 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6488 (tm-30) REVERT: J 73 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7996 (tt) REVERT: J 79 GLU cc_start: 0.7407 (tp30) cc_final: 0.7162 (tp30) REVERT: K 33 SER cc_start: 0.8635 (m) cc_final: 0.8313 (t) REVERT: K 82 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: K 109 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7933 (mptp) REVERT: L 64 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7734 (ttpp) REVERT: M 20 LYS cc_start: 0.8170 (pttm) cc_final: 0.7923 (pttm) REVERT: M 119 LYS cc_start: 0.8300 (ttmm) cc_final: 0.7930 (ttmm) REVERT: M 156 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8143 (m) REVERT: N 11 VAL cc_start: 0.7558 (OUTLIER) cc_final: 0.7173 (t) REVERT: O 217 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5965 (tp30) outliers start: 154 outliers final: 109 residues processed: 908 average time/residue: 0.1656 time to fit residues: 235.6155 Evaluate side-chains 934 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 805 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 117 TYR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 GLN Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 226 THR Chi-restraints excluded: chain J residue 238 SER Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 167 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 203 GLU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 151 TYR Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 217 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 226 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 318 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 252 optimal weight: 0.0870 chunk 198 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 28 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 GLN ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 GLN ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.136960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115620 restraints weight = 38581.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119617 restraints weight = 18480.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.122269 restraints weight = 10877.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.123741 restraints weight = 7445.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124986 restraints weight = 5825.295| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28263 Z= 0.208 Angle : 0.593 8.610 38188 Z= 0.315 Chirality : 0.045 0.198 4371 Planarity : 0.003 0.054 4899 Dihedral : 5.346 55.391 3779 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.90 % Favored : 89.81 % Rotamer: Outliers : 5.90 % Allowed : 35.04 % Favored : 59.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.14), residues: 3473 helix: -2.13 (0.55), residues: 82 sheet: -0.19 (0.14), residues: 1601 loop : -2.33 (0.13), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 239 TYR 0.031 0.002 TYR C 51 PHE 0.027 0.002 PHE H 195 TRP 0.007 0.001 TRP M 72 HIS 0.004 0.001 HIS I 94 Details of bonding type rmsd covalent geometry : bond 0.00495 (28263) covalent geometry : angle 0.59335 (38188) hydrogen bonds : bond 0.03393 ( 183) hydrogen bonds : angle 5.13628 ( 504) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 861 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4826 (OUTLIER) cc_final: 0.3278 (tp30) REVERT: A 79 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7053 (tm-30) REVERT: A 125 LYS cc_start: 0.8261 (ttpp) cc_final: 0.7992 (tttp) REVERT: B 69 ASP cc_start: 0.6521 (OUTLIER) cc_final: 0.6006 (m-30) REVERT: B 84 GLU cc_start: 0.7006 (mp0) cc_final: 0.6571 (mp0) REVERT: B 217 GLU cc_start: 0.6932 (pm20) cc_final: 0.6659 (pm20) REVERT: B 235 ILE cc_start: 0.8231 (mt) cc_final: 0.7977 (mp) REVERT: C 21 LEU cc_start: 0.8250 (tp) cc_final: 0.8000 (tt) REVERT: C 26 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6563 (tm-30) REVERT: C 54 LYS cc_start: 0.7948 (mttp) cc_final: 0.7536 (mttm) REVERT: C 146 LYS cc_start: 0.8983 (mmmt) cc_final: 0.8436 (mmmt) REVERT: C 185 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5133 (mp0) REVERT: D 54 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7457 (mmmt) REVERT: D 69 ASP cc_start: 0.7554 (t0) cc_final: 0.7310 (t0) REVERT: D 135 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.8001 (p) REVERT: D 155 LYS cc_start: 0.7774 (mttt) cc_final: 0.7540 (mttt) REVERT: E 26 GLU cc_start: 0.6693 (tp30) cc_final: 0.6378 (tp30) REVERT: E 120 LYS cc_start: 0.8217 (mptt) cc_final: 0.7717 (ptpp) REVERT: E 198 VAL cc_start: 0.8392 (p) cc_final: 0.8181 (t) REVERT: E 205 GLU cc_start: 0.6931 (tm-30) cc_final: 0.6435 (tm-30) REVERT: E 210 ASN cc_start: 0.8325 (t0) cc_final: 0.7883 (t0) REVERT: E 223 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8371 (mp) REVERT: E 236 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6857 (mt-10) REVERT: F 84 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6597 (tm-30) REVERT: F 103 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6444 (tppp) REVERT: G 21 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7312 (tm) REVERT: G 26 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7262 (mm-30) REVERT: G 71 GLU cc_start: 0.7326 (mp0) cc_final: 0.6812 (mp0) REVERT: G 83 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: G 86 LYS cc_start: 0.8111 (mtpt) cc_final: 0.7855 (mtpp) REVERT: G 109 LYS cc_start: 0.8189 (mtmm) cc_final: 0.7915 (mppt) REVERT: G 197 ASN cc_start: 0.7466 (t0) cc_final: 0.7245 (t0) REVERT: G 205 GLU cc_start: 0.6571 (tm-30) cc_final: 0.6195 (tm-30) REVERT: H 88 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7815 (tmtt) REVERT: H 109 LYS cc_start: 0.7304 (ptmm) cc_final: 0.7084 (ptmm) REVERT: H 186 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: H 209 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6898 (mm-30) REVERT: I 109 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8099 (mmtt) REVERT: I 163 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7963 (mmmm) REVERT: J 6 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7778 (pt0) REVERT: J 24 THR cc_start: 0.8207 (m) cc_final: 0.7905 (t) REVERT: J 26 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6452 (tm-30) REVERT: J 73 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8082 (tt) REVERT: K 82 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: L 113 ASP cc_start: 0.6954 (t0) cc_final: 0.6684 (t0) REVERT: L 125 LYS cc_start: 0.8406 (mtpt) cc_final: 0.8163 (mtpt) REVERT: M 119 LYS cc_start: 0.8272 (ttmm) cc_final: 0.7918 (ttmm) REVERT: M 156 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8144 (m) REVERT: M 236 GLU cc_start: 0.7636 (tt0) cc_final: 0.7411 (tt0) REVERT: N 11 VAL cc_start: 0.7753 (OUTLIER) cc_final: 0.7403 (t) REVERT: N 91 ASP cc_start: 0.7481 (t0) cc_final: 0.7281 (t0) outliers start: 178 outliers final: 125 residues processed: 961 average time/residue: 0.1707 time to fit residues: 257.9081 Evaluate side-chains 1001 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 855 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 117 TYR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 32 PHE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 163 LYS Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 226 THR Chi-restraints excluded: chain J residue 238 SER Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 167 PHE Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 169 GLU Chi-restraints excluded: chain M residue 203 GLU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 15 ARG Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 151 TYR Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 201 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 46 optimal weight: 0.9990 chunk 329 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 342 optimal weight: 0.7980 chunk 344 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN E 28 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116195 restraints weight = 38701.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120199 restraints weight = 18562.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.122799 restraints weight = 10988.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124575 restraints weight = 7504.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.125580 restraints weight = 5710.372| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28263 Z= 0.141 Angle : 0.563 9.045 38188 Z= 0.297 Chirality : 0.044 0.207 4371 Planarity : 0.003 0.053 4899 Dihedral : 5.183 58.901 3779 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.41 % Favored : 91.33 % Rotamer: Outliers : 5.23 % Allowed : 36.17 % Favored : 58.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.14), residues: 3473 helix: -2.06 (0.55), residues: 82 sheet: -0.18 (0.14), residues: 1592 loop : -2.33 (0.13), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 239 TYR 0.023 0.001 TYR C 51 PHE 0.017 0.002 PHE B 32 TRP 0.004 0.001 TRP M 72 HIS 0.003 0.001 HIS I 94 Details of bonding type rmsd covalent geometry : bond 0.00337 (28263) covalent geometry : angle 0.56250 (38188) hydrogen bonds : bond 0.02933 ( 183) hydrogen bonds : angle 5.01060 ( 504) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 828 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4774 (OUTLIER) cc_final: 0.3831 (tp30) REVERT: A 79 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7067 (tm-30) REVERT: A 125 LYS cc_start: 0.8263 (ttpp) cc_final: 0.8016 (tttp) REVERT: B 26 GLU cc_start: 0.7308 (pm20) cc_final: 0.7101 (pm20) REVERT: B 69 ASP cc_start: 0.6535 (OUTLIER) cc_final: 0.5999 (m-30) REVERT: B 84 GLU cc_start: 0.7013 (mp0) cc_final: 0.6627 (mp0) REVERT: B 174 GLU cc_start: 0.7469 (tt0) cc_final: 0.7000 (tt0) REVERT: B 217 GLU cc_start: 0.6928 (pm20) cc_final: 0.6700 (pm20) REVERT: B 235 ILE cc_start: 0.8221 (mt) cc_final: 0.7959 (mp) REVERT: C 21 LEU cc_start: 0.8246 (tp) cc_final: 0.7985 (tt) REVERT: C 54 LYS cc_start: 0.7920 (mttp) cc_final: 0.7488 (mttm) REVERT: C 185 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.4966 (mp0) REVERT: D 54 LYS cc_start: 0.7890 (mmmt) cc_final: 0.7451 (mmmt) REVERT: D 69 ASP cc_start: 0.7529 (t0) cc_final: 0.7300 (t0) REVERT: D 135 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.7985 (p) REVERT: D 155 LYS cc_start: 0.7761 (mttt) cc_final: 0.7511 (mttt) REVERT: E 26 GLU cc_start: 0.6741 (tp30) cc_final: 0.6409 (tp30) REVERT: E 107 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6632 (ptmt) REVERT: E 120 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7701 (ptpp) REVERT: E 198 VAL cc_start: 0.8374 (p) cc_final: 0.8160 (t) REVERT: E 205 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6440 (tm-30) REVERT: E 210 ASN cc_start: 0.8303 (t0) cc_final: 0.7889 (t0) REVERT: E 223 LEU cc_start: 0.8709 (mp) cc_final: 0.8432 (mp) REVERT: E 236 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6722 (mt-10) REVERT: F 84 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6554 (tm-30) REVERT: F 103 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6469 (tppp) REVERT: G 21 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7321 (tm) REVERT: G 26 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: G 64 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7441 (mtpp) REVERT: G 71 GLU cc_start: 0.7307 (mp0) cc_final: 0.6849 (mp0) REVERT: G 86 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7763 (mtpp) REVERT: G 205 GLU cc_start: 0.6556 (tm-30) cc_final: 0.6243 (tm-30) REVERT: H 88 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7856 (tmtt) REVERT: H 186 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: H 209 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6962 (mm-30) REVERT: I 109 LYS cc_start: 0.8347 (mmtt) cc_final: 0.8072 (mmtt) REVERT: J 6 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7706 (pt0) REVERT: J 56 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6138 (tm-30) REVERT: J 73 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8029 (tt) REVERT: K 82 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7680 (pm20) REVERT: M 20 LYS cc_start: 0.8184 (pttm) cc_final: 0.7927 (pttm) REVERT: M 119 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7920 (ttmm) REVERT: M 156 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8127 (m) REVERT: M 236 GLU cc_start: 0.7599 (tt0) cc_final: 0.7386 (tt0) REVERT: N 11 VAL cc_start: 0.7607 (OUTLIER) cc_final: 0.7234 (t) REVERT: O 241 GLU cc_start: 0.6801 (pp20) cc_final: 0.6556 (pp20) outliers start: 158 outliers final: 116 residues processed: 913 average time/residue: 0.1742 time to fit residues: 248.8286 Evaluate side-chains 968 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 832 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 117 TYR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 226 THR Chi-restraints excluded: chain J residue 238 SER Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 167 PHE Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 203 GLU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 151 TYR Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 201 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 11 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 146 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 273 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 250 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 28 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 ASN ** 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 = 0.3677 r_free = 0.3677 target = 0.135887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113507 restraints weight = 39409.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.117722 restraints weight = 18178.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120411 restraints weight = 10548.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122151 restraints weight = 7223.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123455 restraints weight = 5495.840| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28263 Z= 0.124 Angle : 0.559 9.739 38188 Z= 0.294 Chirality : 0.044 0.214 4371 Planarity : 0.003 0.051 4899 Dihedral : 4.959 52.361 3776 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.75 % Favored : 90.99 % Rotamer: Outliers : 4.84 % Allowed : 36.63 % Favored : 58.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.14), residues: 3473 helix: -1.94 (0.55), residues: 82 sheet: -0.16 (0.14), residues: 1589 loop : -2.29 (0.13), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 15 TYR 0.022 0.001 TYR C 51 PHE 0.016 0.001 PHE A 195 TRP 0.004 0.001 TRP M 72 HIS 0.002 0.001 HIS I 94 Details of bonding type rmsd covalent geometry : bond 0.00293 (28263) covalent geometry : angle 0.55923 (38188) hydrogen bonds : bond 0.02751 ( 183) hydrogen bonds : angle 4.89340 ( 504) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 824 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4621 (OUTLIER) cc_final: 0.3715 (tp30) REVERT: A 79 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7089 (tm-30) REVERT: A 125 LYS cc_start: 0.8256 (ttpp) cc_final: 0.7990 (tttp) REVERT: B 69 ASP cc_start: 0.6548 (OUTLIER) cc_final: 0.5993 (m-30) REVERT: B 84 GLU cc_start: 0.7015 (mp0) cc_final: 0.6626 (mp0) REVERT: B 217 GLU cc_start: 0.6970 (pm20) cc_final: 0.6716 (pm20) REVERT: B 235 ILE cc_start: 0.8207 (mt) cc_final: 0.7956 (mp) REVERT: C 21 LEU cc_start: 0.8272 (tp) cc_final: 0.7995 (tt) REVERT: C 26 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6525 (tm-30) REVERT: C 185 GLU cc_start: 0.5632 (OUTLIER) cc_final: 0.4793 (mp0) REVERT: D 54 LYS cc_start: 0.7920 (mmmt) cc_final: 0.7459 (mmmt) REVERT: D 69 ASP cc_start: 0.7513 (t0) cc_final: 0.7232 (t0) REVERT: D 135 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8002 (p) REVERT: D 155 LYS cc_start: 0.7748 (mttt) cc_final: 0.7499 (mttt) REVERT: E 26 GLU cc_start: 0.6774 (tp30) cc_final: 0.6390 (tp30) REVERT: E 107 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6655 (ptmt) REVERT: E 198 VAL cc_start: 0.8357 (p) cc_final: 0.8107 (t) REVERT: E 210 ASN cc_start: 0.8316 (t0) cc_final: 0.7900 (t0) REVERT: E 236 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6745 (mt-10) REVERT: F 84 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6614 (tm-30) REVERT: F 103 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6436 (tppp) REVERT: G 21 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7338 (tm) REVERT: G 26 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7307 (mm-30) REVERT: G 64 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7443 (mtpp) REVERT: G 71 GLU cc_start: 0.7362 (mp0) cc_final: 0.6907 (mp0) REVERT: G 86 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7786 (mtpp) REVERT: G 205 GLU cc_start: 0.6608 (tm-30) cc_final: 0.6258 (tm-30) REVERT: H 88 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7792 (tmtt) REVERT: H 186 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6520 (mp0) REVERT: H 209 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6927 (mm-30) REVERT: I 109 LYS cc_start: 0.8361 (mmtt) cc_final: 0.8076 (mmtt) REVERT: J 6 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7690 (pt0) REVERT: J 26 GLU cc_start: 0.6698 (tm-30) cc_final: 0.6426 (tm-30) REVERT: J 73 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7974 (tt) REVERT: J 79 GLU cc_start: 0.7442 (tp30) cc_final: 0.7194 (tp30) REVERT: K 82 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: K 123 THR cc_start: 0.8665 (m) cc_final: 0.8425 (p) REVERT: K 166 LYS cc_start: 0.6241 (OUTLIER) cc_final: 0.6008 (ptmm) REVERT: L 154 GLU cc_start: 0.6822 (mp0) cc_final: 0.6530 (mp0) REVERT: M 20 LYS cc_start: 0.8178 (pttm) cc_final: 0.7919 (pttm) REVERT: M 119 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7978 (ttmm) REVERT: M 156 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8098 (m) REVERT: M 236 GLU cc_start: 0.7614 (tt0) cc_final: 0.7391 (tt0) REVERT: N 11 VAL cc_start: 0.7525 (OUTLIER) cc_final: 0.7181 (t) REVERT: N 79 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7291 (mm-30) REVERT: O 241 GLU cc_start: 0.6602 (pp20) cc_final: 0.6361 (pp20) outliers start: 146 outliers final: 111 residues processed: 911 average time/residue: 0.1571 time to fit residues: 225.3177 Evaluate side-chains 948 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 818 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 117 TYR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 226 THR Chi-restraints excluded: chain J residue 238 SER Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 167 PHE Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 203 GLU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 151 TYR Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 201 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 125 optimal weight: 1.9990 chunk 262 optimal weight: 0.6980 chunk 213 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 289 optimal weight: 0.0770 chunk 272 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 227 optimal weight: 0.0170 chunk 102 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 28 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.136714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114299 restraints weight = 39400.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118552 restraints weight = 18238.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121276 restraints weight = 10545.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123108 restraints weight = 7191.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124150 restraints weight = 5421.813| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28263 Z= 0.108 Angle : 0.547 9.343 38188 Z= 0.287 Chirality : 0.044 0.197 4371 Planarity : 0.003 0.061 4899 Dihedral : 4.820 42.914 3776 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.86 % Favored : 91.91 % Rotamer: Outliers : 4.41 % Allowed : 37.03 % Favored : 58.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.14), residues: 3473 helix: -1.84 (0.55), residues: 82 sheet: -0.12 (0.14), residues: 1593 loop : -2.24 (0.13), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 239 TYR 0.020 0.001 TYR C 51 PHE 0.014 0.001 PHE B 32 TRP 0.004 0.001 TRP I 72 HIS 0.002 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00255 (28263) covalent geometry : angle 0.54699 (38188) hydrogen bonds : bond 0.02593 ( 183) hydrogen bonds : angle 4.78104 ( 504) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6946 Ramachandran restraints generated. 3473 Oldfield, 0 Emsley, 3473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 825 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4551 (OUTLIER) cc_final: 0.3685 (tp30) REVERT: A 79 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7090 (tm-30) REVERT: A 125 LYS cc_start: 0.8240 (ttpp) cc_final: 0.7975 (tttp) REVERT: B 69 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6006 (m-30) REVERT: B 84 GLU cc_start: 0.7016 (mp0) cc_final: 0.6584 (mp0) REVERT: B 217 GLU cc_start: 0.7015 (pm20) cc_final: 0.6762 (pm20) REVERT: B 235 ILE cc_start: 0.8204 (mt) cc_final: 0.7968 (mp) REVERT: C 26 GLU cc_start: 0.6821 (tm-30) cc_final: 0.6467 (tm-30) REVERT: C 53 LEU cc_start: 0.8182 (tp) cc_final: 0.7815 (tt) REVERT: C 54 LYS cc_start: 0.7891 (mttp) cc_final: 0.7560 (mttm) REVERT: C 185 GLU cc_start: 0.5421 (OUTLIER) cc_final: 0.4696 (mp0) REVERT: D 54 LYS cc_start: 0.7890 (mmmt) cc_final: 0.7441 (mmmt) REVERT: D 69 ASP cc_start: 0.7501 (t0) cc_final: 0.7238 (t0) REVERT: D 135 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.7981 (p) REVERT: D 155 LYS cc_start: 0.7744 (mttt) cc_final: 0.6831 (tptt) REVERT: E 26 GLU cc_start: 0.6763 (tp30) cc_final: 0.6379 (tp30) REVERT: E 107 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6665 (ptmt) REVERT: E 120 LYS cc_start: 0.8219 (mptt) cc_final: 0.7692 (ptpp) REVERT: E 198 VAL cc_start: 0.8355 (p) cc_final: 0.8083 (t) REVERT: E 210 ASN cc_start: 0.8295 (t0) cc_final: 0.7911 (t0) REVERT: E 236 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: F 84 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6613 (tm-30) REVERT: F 103 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6427 (tppp) REVERT: G 21 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7327 (tm) REVERT: G 71 GLU cc_start: 0.7395 (mp0) cc_final: 0.7016 (mp0) REVERT: G 91 ASP cc_start: 0.8223 (t0) cc_final: 0.7972 (t70) REVERT: G 205 GLU cc_start: 0.6606 (tm-30) cc_final: 0.6235 (tm-30) REVERT: H 51 TYR cc_start: 0.7212 (m-10) cc_final: 0.6458 (m-10) REVERT: H 88 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7546 (tttm) REVERT: H 186 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: I 109 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8068 (mmtt) REVERT: J 6 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7720 (pt0) REVERT: J 26 GLU cc_start: 0.6673 (tm-30) cc_final: 0.6451 (tm-30) REVERT: J 79 GLU cc_start: 0.7419 (tp30) cc_final: 0.7181 (tp30) REVERT: J 236 GLU cc_start: 0.7328 (tt0) cc_final: 0.6974 (tt0) REVERT: K 123 THR cc_start: 0.8662 (m) cc_final: 0.8431 (p) REVERT: L 154 GLU cc_start: 0.6826 (mp0) cc_final: 0.6536 (mp0) REVERT: M 20 LYS cc_start: 0.8130 (pttm) cc_final: 0.7877 (pttm) REVERT: M 119 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7958 (ttmm) REVERT: M 156 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8085 (m) REVERT: N 11 VAL cc_start: 0.7406 (OUTLIER) cc_final: 0.7129 (t) REVERT: N 79 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7283 (mm-30) outliers start: 133 outliers final: 112 residues processed: 905 average time/residue: 0.1680 time to fit residues: 239.4944 Evaluate side-chains 947 residues out of total 3019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 820 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 117 TYR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 PHE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 GLN Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 238 SER Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 167 PHE Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 203 GLU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 151 TYR Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 79 GLU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 201 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 63 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 155 optimal weight: 0.0060 chunk 21 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 277 optimal weight: 0.0010 chunk 18 optimal weight: 0.0980 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 28 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 ASN ** O 210 ASN ** 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 = 0.3697 r_free = 0.3697 target = 0.137475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.115167 restraints weight = 39365.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119379 restraints weight = 18390.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122108 restraints weight = 10681.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123948 restraints weight = 7250.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125049 restraints weight = 5484.208| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 28263 Z= 0.096 Angle : 0.535 9.270 38188 Z= 0.280 Chirality : 0.043 0.181 4371 Planarity : 0.003 0.049 4899 Dihedral : 4.643 40.852 3776 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.86 % Favored : 91.91 % Rotamer: Outliers : 4.31 % Allowed : 37.36 % Favored : 58.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.14), residues: 3473 helix: -1.71 (0.55), residues: 82 sheet: -0.07 (0.14), residues: 1589 loop : -2.19 (0.13), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 239 TYR 0.019 0.001 TYR C 51 PHE 0.013 0.001 PHE B 32 TRP 0.004 0.001 TRP I 72 HIS 0.002 0.001 HIS I 94 Details of bonding type rmsd covalent geometry : bond 0.00225 (28263) covalent geometry : angle 0.53543 (38188) hydrogen bonds : bond 0.02429 ( 183) hydrogen bonds : angle 4.65988 ( 504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5301.69 seconds wall clock time: 92 minutes 11.31 seconds (5531.31 seconds total)