Starting phenix.real_space_refine on Thu Feb 5 12:15:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mth_48609/02_2026/9mth_48609.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mth_48609/02_2026/9mth_48609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mth_48609/02_2026/9mth_48609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mth_48609/02_2026/9mth_48609.map" model { file = "/net/cci-nas-00/data/ceres_data/9mth_48609/02_2026/9mth_48609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mth_48609/02_2026/9mth_48609.cif" } resolution = 2.5 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= 0.001 sd= 0.019 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 81 5.16 5 C 10713 2.51 5 N 2942 2.21 5 O 3324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17060 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2520 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain: "B" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1382 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "C" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2517 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 300} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1382 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "E" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2490 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 20, 'TRANS': 296} Chain breaks: 1 Chain: "F" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1382 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "H" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 978 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 984 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "J" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 827 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 10, 'TRANS': 102} Chain: "L" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 827 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 10, 'TRANS': 102} Chain: "M" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 978 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "N" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 793 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 9, 'TRANS': 98} Time building chain proxies: 3.30, per 1000 atoms: 0.19 Number of scatterers: 17060 At special positions: 0 Unit cell: (122.728, 138.598, 147.062, 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 81 16.00 O 3324 8.00 N 2942 7.00 C 10713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.04 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.01 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.04 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.04 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.04 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 98 " - pdb=" SG CYS H 100E" distance=2.03 Simple disulfide: pdb=" SG CYS I 98 " - pdb=" SG CYS I 100E" distance=2.05 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 98 " - pdb=" SG CYS M 100E" distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 528.4 milliseconds 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3976 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 52 sheets defined 19.9% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 37 through 57 Processing helix chain 'B' and resid 74 through 127 removed outlier: 3.718A pdb=" N GLU B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 171 removed outlier: 4.180A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 58 removed outlier: 3.560A pdb=" N LYS D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 127 removed outlier: 3.767A pdb=" N GLU D 78 " --> pdb=" O GLU D 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'F' and resid 37 through 57 Processing helix chain 'F' and resid 74 through 127 removed outlier: 3.790A pdb=" N GLU F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 171 removed outlier: 4.087A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.111A pdb=" N ASP H 31 " --> pdb=" O ASP H 28 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN H 32 " --> pdb=" O LEU H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.311A pdb=" N ASP I 31 " --> pdb=" O ASP I 28 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN I 32 " --> pdb=" O LEU I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.544A pdb=" N ASP J 82 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 79 through 83' Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.876A pdb=" N ASP M 31 " --> pdb=" O ASP M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.722A pdb=" N THR M 87 " --> pdb=" O THR M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.883A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.585A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 115 through 121A removed outlier: 3.906A pdb=" N SER A 117 " --> pdb=" O SER A 260A" (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 8.024A pdb=" N SER A 138 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N GLU A 144 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 removed outlier: 4.019A pdb=" N THR B 64 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 33 through 36 removed outlier: 6.250A pdb=" N CYS D 137 " --> pdb=" O ILE D 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 53A removed outlier: 6.508A pdb=" N LEU C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.425A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 115 through 121A removed outlier: 3.771A pdb=" N SER C 117 " --> pdb=" O SER C 260A" (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC2, first strand: chain 'C' and resid 136 through 140 Processing sheet with id=AC3, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC4, first strand: chain 'C' and resid 166 through 169 Processing sheet with id=AC5, first strand: chain 'C' and resid 286 through 288 removed outlier: 3.901A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 32 through 36 Processing sheet with id=AC7, first strand: chain 'E' and resid 24 through 26 removed outlier: 4.054A pdb=" N ASP E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC9, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'E' and resid 51 through 53A removed outlier: 5.890A pdb=" N LEU E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.487A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 115 through 121A removed outlier: 6.209A pdb=" N SER E 260A" --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE E 118 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA E 259 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG E 120 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA E 257 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU E 175 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD5, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.476A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD7, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD8, first strand: chain 'E' and resid 286 through 288 removed outlier: 3.874A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.694A pdb=" N SER H 112 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.694A pdb=" N SER H 112 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 99 through 100 Processing sheet with id=AE4, first strand: chain 'I' and resid 3 through 7 removed outlier: 6.223A pdb=" N GLY I 16 " --> pdb=" O SER I 82B" (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.820A pdb=" N PHE I 34 " --> pdb=" O THR I 50 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.620A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 3 through 4 Processing sheet with id=AE8, first strand: chain 'J' and resid 8 through 13 removed outlier: 6.535A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 3 through 4 Processing sheet with id=AF1, first strand: chain 'L' and resid 8 through 13 removed outlier: 7.016A pdb=" N MET L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'M' and resid 11 through 13 removed outlier: 3.695A pdb=" N SER M 112 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE M 34 " --> pdb=" O THR M 50 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR M 50 " --> pdb=" O PHE M 34 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 11 through 13 removed outlier: 3.695A pdb=" N SER M 112 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 99 through 100 Processing sheet with id=AF6, first strand: chain 'N' and resid 3 through 4 Processing sheet with id=AF7, first strand: chain 'N' and resid 8 through 13 removed outlier: 6.895A pdb=" N MET N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP N 35 " --> pdb=" O VAL N 47 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1797 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: 2.72 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5628 1.35 - 1.47: 4446 1.47 - 1.60: 7284 1.60 - 1.72: 0 1.72 - 1.85: 108 Bond restraints: 17466 Sorted by residual: bond pdb=" C ASN B 71 " pdb=" N LYS B 72 " ideal model delta sigma weight residual 1.335 1.435 -0.100 1.31e-02 5.83e+03 5.85e+01 bond pdb=" C LYS C 313 " pdb=" N LEU C 314 " ideal model delta sigma weight residual 1.333 1.259 0.074 1.30e-02 5.92e+03 3.26e+01 bond pdb=" C LYS B 72 " pdb=" N LEU B 73 " ideal model delta sigma weight residual 1.334 1.256 0.078 1.38e-02 5.25e+03 3.24e+01 bond pdb=" C MET I 100J" pdb=" N ASP I 101 " ideal model delta sigma weight residual 1.331 1.398 -0.068 1.38e-02 5.25e+03 2.40e+01 bond pdb=" C LEU C 314 " pdb=" N ARG C 315 " ideal model delta sigma weight residual 1.330 1.269 0.060 1.32e-02 5.74e+03 2.08e+01 ... (remaining 17461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 23050 2.08 - 4.16: 569 4.16 - 6.24: 60 6.24 - 8.32: 11 8.32 - 10.40: 4 Bond angle restraints: 23694 Sorted by residual: angle pdb=" N SER C 291 " pdb=" CA SER C 291 " pdb=" C SER C 291 " ideal model delta sigma weight residual 113.16 105.19 7.97 1.24e+00 6.50e-01 4.13e+01 angle pdb=" CA PHE E 258 " pdb=" CB PHE E 258 " pdb=" CG PHE E 258 " ideal model delta sigma weight residual 113.80 119.22 -5.42 1.00e+00 1.00e+00 2.94e+01 angle pdb=" O GLY I 100I" pdb=" C GLY I 100I" pdb=" N MET I 100J" ideal model delta sigma weight residual 122.86 128.22 -5.36 1.00e+00 1.00e+00 2.88e+01 angle pdb=" C PRO J 59 " pdb=" CA PRO J 59 " pdb=" CB PRO J 59 " ideal model delta sigma weight residual 111.56 102.95 8.61 1.65e+00 3.67e-01 2.73e+01 angle pdb=" C LYS C 90 " pdb=" N PRO C 91 " pdb=" CA PRO C 91 " ideal model delta sigma weight residual 119.32 125.10 -5.78 1.14e+00 7.69e-01 2.57e+01 ... (remaining 23689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9035 17.86 - 35.72: 966 35.72 - 53.58: 265 53.58 - 71.44: 72 71.44 - 89.31: 25 Dihedral angle restraints: 10363 sinusoidal: 4098 harmonic: 6265 Sorted by residual: dihedral pdb=" CD ARG A 261 " pdb=" NE ARG A 261 " pdb=" CZ ARG A 261 " pdb=" NH1 ARG A 261 " ideal model delta sinusoidal sigma weight residual 0.00 89.31 -89.31 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CD ARG E 261 " pdb=" NE ARG E 261 " pdb=" CZ ARG E 261 " pdb=" NH1 ARG E 261 " ideal model delta sinusoidal sigma weight residual 0.00 86.04 -86.04 1 1.00e+01 1.00e-02 8.94e+01 dihedral pdb=" CB CYS M 98 " pdb=" SG CYS M 98 " pdb=" SG CYS M 100E" pdb=" CB CYS M 100E" ideal model delta sinusoidal sigma weight residual 93.00 175.64 -82.64 1 1.00e+01 1.00e-02 8.37e+01 ... (remaining 10360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2098 0.059 - 0.118: 376 0.118 - 0.177: 40 0.177 - 0.237: 14 0.237 - 0.296: 5 Chirality restraints: 2533 Sorted by residual: chirality pdb=" CA LYS A 90 " pdb=" N LYS A 90 " pdb=" C LYS A 90 " pdb=" CB LYS A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ARG J 61 " pdb=" N ARG J 61 " pdb=" C ARG J 61 " pdb=" CB ARG J 61 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA LYS C 90 " pdb=" N LYS C 90 " pdb=" C LYS C 90 " pdb=" CB LYS C 90 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2530 not shown) Planarity restraints: 3097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 261 " 1.132 9.50e-02 1.11e+02 5.07e-01 1.55e+02 pdb=" NE ARG A 261 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 261 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 261 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 261 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 261 " 1.107 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG E 261 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG E 261 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG E 261 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG E 261 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 192 " 1.079 9.50e-02 1.11e+02 4.84e-01 1.41e+02 pdb=" NE ARG C 192 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG C 192 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 192 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 192 " 0.020 2.00e-02 2.50e+03 ... (remaining 3094 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 64 2.50 - 3.10: 11837 3.10 - 3.70: 25417 3.70 - 4.30: 38208 4.30 - 4.90: 65505 Nonbonded interactions: 141031 Sorted by model distance: nonbonded pdb=" O LYS N 92 " pdb=" OD1 ASN N 93 " model vdw 1.906 3.040 nonbonded pdb=" NZ LYS A 197 " pdb=" CB ASN A 248 " model vdw 2.122 3.520 nonbonded pdb=" OH TYR F 119 " pdb=" OE1 GLU F 132 " model vdw 2.131 3.040 nonbonded pdb=" NZ LYS E 197 " pdb=" CB ASN E 248 " model vdw 2.192 3.520 nonbonded pdb=" OG SER C 114 " pdb=" O PHE C 263 " model vdw 2.199 3.040 ... (remaining 141026 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 11 through 77 or resid 81A through 324)) selection = (chain 'C' and (resid 11 through 77 or resid 81A through 324)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = (chain 'I' and resid 2 through 114) selection = chain 'M' } ncs_group { reference = (chain 'J' and resid 2 through 106A) selection = (chain 'L' and resid 2 through 106A) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.310 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.005 0.100 17490 Z= 0.293 Angle : 0.742 10.400 23742 Z= 0.453 Chirality : 0.050 0.296 2533 Planarity : 0.019 0.507 3097 Dihedral : 16.555 89.305 6315 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.82 % Allowed : 18.87 % Favored : 79.30 % Cbeta Deviations : 0.10 % 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 are not related in a simple way. whole: -0.47 (0.17), residues: 2162 helix: 1.10 (0.27), residues: 373 sheet: 0.74 (0.24), residues: 453 loop : -1.17 (0.15), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 261 TYR 0.016 0.001 TYR F 159 PHE 0.014 0.002 PHE N 62 TRP 0.008 0.001 TRP F 21 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00515 (17466) covalent geometry : angle 0.73858 (23694) SS BOND : bond 0.00731 ( 24) SS BOND : angle 1.64000 ( 48) hydrogen bonds : bond 0.14342 ( 664) hydrogen bonds : angle 6.98922 ( 1797) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 385 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 75 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5680 (pt0) REVERT: E 260 SER cc_start: 0.8103 (t) cc_final: 0.7831 (p) REVERT: E 271 ASN cc_start: 0.8510 (p0) cc_final: 0.8292 (p0) REVERT: I 100 CYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6452 (p) REVERT: L 60 SER cc_start: 0.8852 (p) cc_final: 0.8617 (t) outliers start: 34 outliers final: 13 residues processed: 407 average time/residue: 0.6276 time to fit residues: 278.1588 Evaluate side-chains 387 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 372 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 96 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 0.0570 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 298 HIS B 28 ASN B 125 GLN C 285 GLN D 95 ASN D 125 GLN E 48 ASN E 73 ASN E 150 ASN E 199 ASN E 269 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN L 38 GLN N 37 GLN N 69 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.114541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.105878 restraints weight = 23803.780| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.57 r_work: 0.3423 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17490 Z= 0.232 Angle : 0.580 10.309 23742 Z= 0.300 Chirality : 0.045 0.147 2533 Planarity : 0.004 0.058 3097 Dihedral : 5.236 54.217 2403 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.54 % Allowed : 18.07 % Favored : 78.39 % 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 are not related in a simple way. whole: -0.23 (0.17), residues: 2162 helix: 1.67 (0.27), residues: 384 sheet: 0.65 (0.24), residues: 451 loop : -1.05 (0.15), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 83 TYR 0.018 0.002 TYR F 159 PHE 0.015 0.002 PHE B 110 TRP 0.011 0.001 TRP I 47 HIS 0.007 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00543 (17466) covalent geometry : angle 0.57515 (23694) SS BOND : bond 0.00559 ( 24) SS BOND : angle 1.71448 ( 48) hydrogen bonds : bond 0.04598 ( 664) hydrogen bonds : angle 5.19789 ( 1797) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 378 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: B 99 LEU cc_start: 0.8357 (tp) cc_final: 0.8037 (tp) REVERT: B 103 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6857 (mt-10) REVERT: D 161 LYS cc_start: 0.8526 (tttt) cc_final: 0.8191 (ttpt) REVERT: E 157 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7976 (ttmm) REVERT: E 260 SER cc_start: 0.8410 (t) cc_final: 0.8206 (p) REVERT: E 271 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8368 (p0) REVERT: I 82 MET cc_start: 0.8429 (mtp) cc_final: 0.8197 (mtm) REVERT: M 37 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8466 (t) outliers start: 66 outliers final: 36 residues processed: 403 average time/residue: 0.6406 time to fit residues: 283.1690 Evaluate side-chains 425 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 386 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 271 ASN Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain N residue 96 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 152 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS B 28 ASN B 95 ASN B 125 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN D 125 GLN E 48 ASN E 269 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN N 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.115787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107147 restraints weight = 24004.566| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.57 r_work: 0.3421 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 17490 Z= 0.199 Angle : 0.558 12.135 23742 Z= 0.289 Chirality : 0.044 0.182 2533 Planarity : 0.004 0.051 3097 Dihedral : 4.782 53.821 2383 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.75 % Allowed : 18.61 % Favored : 77.64 % 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 are not related in a simple way. whole: -0.12 (0.17), residues: 2162 helix: 1.89 (0.26), residues: 378 sheet: 0.65 (0.23), residues: 451 loop : -0.97 (0.15), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.018 0.002 TYR I 100F PHE 0.014 0.001 PHE D 9 TRP 0.012 0.001 TRP I 47 HIS 0.006 0.001 HIS I 99 Details of bonding type rmsd covalent geometry : bond 0.00468 (17466) covalent geometry : angle 0.54694 (23694) SS BOND : bond 0.00579 ( 24) SS BOND : angle 2.53408 ( 48) hydrogen bonds : bond 0.04256 ( 664) hydrogen bonds : angle 5.03393 ( 1797) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 393 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 143 LYS cc_start: 0.8563 (mmmm) cc_final: 0.8267 (mmmm) REVERT: D 11 GLU cc_start: 0.7523 (mp0) cc_final: 0.7304 (mp0) REVERT: D 77 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7674 (mmt) REVERT: D 150 GLU cc_start: 0.7383 (tp30) cc_final: 0.7179 (mp0) REVERT: D 161 LYS cc_start: 0.8495 (tttt) cc_final: 0.8183 (ttpt) REVERT: E 157 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.7992 (ttmm) REVERT: F 19 ASP cc_start: 0.8344 (p0) cc_final: 0.8088 (p0) REVERT: F 58 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8696 (tptt) REVERT: H 32 ASN cc_start: 0.8595 (m-40) cc_final: 0.8384 (m110) REVERT: I 82 MET cc_start: 0.8440 (mtp) cc_final: 0.8233 (mtm) REVERT: M 98 CYS cc_start: 0.7352 (p) cc_final: 0.7017 (p) outliers start: 70 outliers final: 40 residues processed: 420 average time/residue: 0.7152 time to fit residues: 328.6209 Evaluate side-chains 421 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 378 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 96 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 153 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 119 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 298 HIS B 95 ASN B 125 GLN B 154 ASN D 28 ASN D 50 ASN D 95 ASN D 125 GLN D 154 ASN E 48 ASN E 282 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN L 69 ASN N 37 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.115671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107244 restraints weight = 23673.044| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.53 r_work: 0.3438 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17490 Z= 0.161 Angle : 0.531 9.791 23742 Z= 0.275 Chirality : 0.043 0.153 2533 Planarity : 0.004 0.049 3097 Dihedral : 4.583 53.543 2383 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.40 % Allowed : 18.55 % Favored : 77.05 % 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 are not related in a simple way. whole: -0.03 (0.17), residues: 2162 helix: 1.97 (0.26), residues: 378 sheet: 0.67 (0.23), residues: 451 loop : -0.90 (0.15), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 83 TYR 0.016 0.001 TYR F 159 PHE 0.014 0.001 PHE D 9 TRP 0.011 0.001 TRP I 47 HIS 0.004 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00379 (17466) covalent geometry : angle 0.52310 (23694) SS BOND : bond 0.00496 ( 24) SS BOND : angle 2.14411 ( 48) hydrogen bonds : bond 0.04004 ( 664) hydrogen bonds : angle 4.84222 ( 1797) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 384 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: B 74 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7903 (pt0) REVERT: B 143 LYS cc_start: 0.8590 (mmmm) cc_final: 0.8306 (mmmm) REVERT: D 11 GLU cc_start: 0.7546 (mp0) cc_final: 0.7109 (mp0) REVERT: D 72 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7842 (mtmt) REVERT: D 103 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7070 (mt-10) REVERT: D 135 ASN cc_start: 0.7522 (t0) cc_final: 0.7211 (t0) REVERT: E 157 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8062 (ttmm) REVERT: F 19 ASP cc_start: 0.8286 (p0) cc_final: 0.8079 (p0) REVERT: F 58 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8724 (tptt) REVERT: I 82 MET cc_start: 0.8439 (mtp) cc_final: 0.8218 (mtm) REVERT: M 100 CYS cc_start: 0.6953 (p) cc_final: 0.6733 (p) outliers start: 82 outliers final: 40 residues processed: 420 average time/residue: 0.7057 time to fit residues: 324.6607 Evaluate side-chains 428 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 383 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 12 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 173 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 150 optimal weight: 0.0270 chunk 191 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 204 optimal weight: 0.4980 chunk 193 optimal weight: 3.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 298 HIS ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 125 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 95 ASN D 125 GLN E 48 ASN E 269 ASN E 282 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN N 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.115157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.106791 restraints weight = 23682.983| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.52 r_work: 0.3428 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17490 Z= 0.193 Angle : 0.545 9.161 23742 Z= 0.281 Chirality : 0.044 0.159 2533 Planarity : 0.004 0.050 3097 Dihedral : 4.500 53.654 2378 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.18 % Allowed : 19.20 % Favored : 76.62 % 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 are not related in a simple way. whole: -0.03 (0.17), residues: 2162 helix: 1.95 (0.26), residues: 378 sheet: 0.72 (0.23), residues: 445 loop : -0.91 (0.15), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 83 TYR 0.017 0.001 TYR F 159 PHE 0.015 0.001 PHE F 9 TRP 0.013 0.001 TRP I 47 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00457 (17466) covalent geometry : angle 0.53770 (23694) SS BOND : bond 0.00516 ( 24) SS BOND : angle 2.04968 ( 48) hydrogen bonds : bond 0.04046 ( 664) hydrogen bonds : angle 4.79592 ( 1797) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 380 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8330 (m-80) REVERT: B 74 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7923 (pt0) REVERT: B 143 LYS cc_start: 0.8583 (mmmm) cc_final: 0.8292 (mmmm) REVERT: D 11 GLU cc_start: 0.7529 (mp0) cc_final: 0.7008 (mp0) REVERT: D 72 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7818 (mtmt) REVERT: D 135 ASN cc_start: 0.7500 (t0) cc_final: 0.6954 (t0) REVERT: E 81 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7101 (mtm110) REVERT: E 157 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8071 (ttmm) REVERT: F 19 ASP cc_start: 0.8295 (p0) cc_final: 0.8056 (p0) REVERT: F 58 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8623 (tptt) REVERT: F 77 MET cc_start: 0.8147 (mmp) cc_final: 0.7415 (mmt) REVERT: H 32 ASN cc_start: 0.8547 (m-40) cc_final: 0.8339 (m110) REVERT: I 82 MET cc_start: 0.8420 (mtp) cc_final: 0.8189 (mtm) outliers start: 78 outliers final: 46 residues processed: 413 average time/residue: 0.6664 time to fit residues: 300.9923 Evaluate side-chains 429 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 377 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 39 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 191 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 168 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 226 GLN A 298 HIS ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 125 GLN C 48 ASN C 289 ASN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 95 ASN D 125 GLN D 154 ASN E 48 ASN E 269 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN F 154 ASN H 81 GLN N 37 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.115574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107247 restraints weight = 23592.024| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.51 r_work: 0.3431 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17490 Z= 0.181 Angle : 0.570 17.271 23742 Z= 0.292 Chirality : 0.044 0.197 2533 Planarity : 0.004 0.049 3097 Dihedral : 4.578 53.389 2378 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.18 % Allowed : 19.68 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 are not related in a simple way. whole: -0.02 (0.17), residues: 2162 helix: 1.80 (0.26), residues: 384 sheet: 0.77 (0.24), residues: 427 loop : -0.86 (0.15), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 83 TYR 0.023 0.001 TYR M 100F PHE 0.014 0.001 PHE D 9 TRP 0.012 0.001 TRP I 47 HIS 0.005 0.001 HIS M 99 Details of bonding type rmsd covalent geometry : bond 0.00427 (17466) covalent geometry : angle 0.54970 (23694) SS BOND : bond 0.00512 ( 24) SS BOND : angle 3.43358 ( 48) hydrogen bonds : bond 0.03987 ( 664) hydrogen bonds : angle 4.77140 ( 1797) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 376 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7339 (tm-30) REVERT: B 22 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8345 (m-80) REVERT: B 143 LYS cc_start: 0.8595 (mmmm) cc_final: 0.8307 (mmmm) REVERT: C 123 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7844 (tttt) REVERT: D 11 GLU cc_start: 0.7516 (mp0) cc_final: 0.6954 (mp0) REVERT: D 72 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7830 (mtmt) REVERT: D 77 MET cc_start: 0.8168 (mmp) cc_final: 0.7840 (mmt) REVERT: D 99 LEU cc_start: 0.8554 (tp) cc_final: 0.8136 (tp) REVERT: D 135 ASN cc_start: 0.7559 (t0) cc_final: 0.6936 (t0) REVERT: D 161 LYS cc_start: 0.8563 (tttt) cc_final: 0.8266 (ttpt) REVERT: E 53 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7979 (mp) REVERT: E 81 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7100 (mtm110) REVERT: E 106 GLU cc_start: 0.8029 (mp0) cc_final: 0.7827 (mp0) REVERT: E 157 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8095 (ttmm) REVERT: F 19 ASP cc_start: 0.8301 (p0) cc_final: 0.8095 (p0) REVERT: F 58 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8644 (tptt) REVERT: F 158 ASP cc_start: 0.7705 (t70) cc_final: 0.7485 (t0) REVERT: H 32 ASN cc_start: 0.8553 (m-40) cc_final: 0.8330 (m110) REVERT: I 82 MET cc_start: 0.8439 (mtp) cc_final: 0.8234 (mtm) outliers start: 78 outliers final: 47 residues processed: 411 average time/residue: 0.6512 time to fit residues: 291.9819 Evaluate side-chains 426 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 372 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 39 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 72 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 205 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 125 GLN C 48 ASN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 95 ASN D 125 GLN E 48 ASN E 199 ASN E 269 ASN F 28 ASN F 95 ASN F 125 GLN H 81 GLN J 38 GLN N 37 GLN N 93 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.114627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.106318 restraints weight = 23634.543| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.51 r_work: 0.3419 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 0.006 0.058 17490 Z= 0.266 Angle : 0.607 10.519 23742 Z= 0.309 Chirality : 0.046 0.159 2533 Planarity : 0.004 0.051 3097 Dihedral : 4.717 53.660 2378 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.24 % Allowed : 20.38 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 are not related in a simple way. whole: -0.11 (0.17), residues: 2162 helix: 1.69 (0.26), residues: 381 sheet: 0.71 (0.23), residues: 451 loop : -0.93 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 220 TYR 0.018 0.002 TYR B 159 PHE 0.017 0.002 PHE F 9 TRP 0.011 0.002 TRP M 47 HIS 0.007 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00629 (17466) covalent geometry : angle 0.59723 (23694) SS BOND : bond 0.00554 ( 24) SS BOND : angle 2.49164 ( 48) hydrogen bonds : bond 0.04295 ( 664) hydrogen bonds : angle 4.88164 ( 1797) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 373 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: B 77 MET cc_start: 0.8085 (mmm) cc_final: 0.7821 (mmt) REVERT: B 98 LEU cc_start: 0.8778 (tp) cc_final: 0.8529 (tp) REVERT: B 143 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8323 (mmmm) REVERT: C 123 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7885 (tttt) REVERT: C 187 ASN cc_start: 0.7984 (p0) cc_final: 0.7753 (p0) REVERT: D 11 GLU cc_start: 0.7577 (mp0) cc_final: 0.6995 (mp0) REVERT: D 72 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7805 (mtmt) REVERT: D 77 MET cc_start: 0.8058 (mmp) cc_final: 0.7740 (mmt) REVERT: D 135 ASN cc_start: 0.7667 (t0) cc_final: 0.7013 (t0) REVERT: E 53 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7962 (mp) REVERT: E 81 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.6910 (mtm110) REVERT: E 149 LYS cc_start: 0.8270 (mmmm) cc_final: 0.8062 (mmmm) REVERT: E 157 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8094 (ttmm) REVERT: E 271 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8422 (p0) REVERT: F 19 ASP cc_start: 0.8299 (p0) cc_final: 0.8092 (p0) REVERT: F 58 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8667 (tptt) REVERT: H 32 ASN cc_start: 0.8594 (m-40) cc_final: 0.8370 (m110) REVERT: I 82 MET cc_start: 0.8436 (mtp) cc_final: 0.8212 (mtm) outliers start: 79 outliers final: 52 residues processed: 412 average time/residue: 0.6663 time to fit residues: 300.1281 Evaluate side-chains 432 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 372 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 271 ASN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 39 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 109 optimal weight: 0.4980 chunk 56 optimal weight: 0.2980 chunk 96 optimal weight: 0.5980 chunk 208 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 141 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 226 GLN A 298 HIS ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 125 GLN D 28 ASN D 50 ASN D 95 ASN D 125 GLN D 154 ASN E 48 ASN E 199 ASN E 269 ASN F 95 ASN F 125 GLN H 81 GLN N 37 GLN N 93 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.116083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.107727 restraints weight = 23666.930| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.53 r_work: 0.3441 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17490 Z= 0.131 Angle : 0.544 9.289 23742 Z= 0.281 Chirality : 0.043 0.150 2533 Planarity : 0.004 0.049 3097 Dihedral : 4.517 52.932 2378 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.91 % Allowed : 20.54 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: 0.03 (0.17), residues: 2162 helix: 1.90 (0.27), residues: 381 sheet: 0.82 (0.24), residues: 427 loop : -0.84 (0.15), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 83 TYR 0.019 0.001 TYR F 159 PHE 0.013 0.001 PHE D 9 TRP 0.010 0.001 TRP I 47 HIS 0.005 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00304 (17466) covalent geometry : angle 0.53685 (23694) SS BOND : bond 0.00478 ( 24) SS BOND : angle 2.01182 ( 48) hydrogen bonds : bond 0.03806 ( 664) hydrogen bonds : angle 4.69999 ( 1797) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 371 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: B 22 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8338 (m-80) REVERT: B 77 MET cc_start: 0.8120 (mmm) cc_final: 0.7761 (mmt) REVERT: B 98 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8481 (tp) REVERT: B 143 LYS cc_start: 0.8585 (mmmm) cc_final: 0.8306 (mmmm) REVERT: C 89 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7544 (tt0) REVERT: D 11 GLU cc_start: 0.7550 (mp0) cc_final: 0.6936 (mp0) REVERT: D 72 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7789 (mtmt) REVERT: D 135 ASN cc_start: 0.7642 (t0) cc_final: 0.6961 (t0) REVERT: D 161 LYS cc_start: 0.8550 (tttt) cc_final: 0.8266 (ttpt) REVERT: E 53 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8012 (mp) REVERT: E 81 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7077 (mtm110) REVERT: E 149 LYS cc_start: 0.8229 (mmmm) cc_final: 0.8011 (mmmm) REVERT: E 157 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8101 (ttmm) REVERT: E 271 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8374 (p0) REVERT: F 19 ASP cc_start: 0.8283 (p0) cc_final: 0.8056 (p0) REVERT: F 58 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8609 (tptt) REVERT: H 32 ASN cc_start: 0.8576 (m-40) cc_final: 0.8361 (m110) outliers start: 73 outliers final: 40 residues processed: 401 average time/residue: 0.7143 time to fit residues: 312.5960 Evaluate side-chains 421 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 373 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 271 ASN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 12 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 131 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 77 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 226 GLN A 289 ASN A 298 HIS ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 125 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 95 ASN D 125 GLN E 48 ASN E 269 ASN F 95 ASN F 125 GLN H 81 GLN I 81 GLN N 37 GLN N 93 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.115443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107090 restraints weight = 23671.116| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.52 r_work: 0.3438 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17490 Z= 0.179 Angle : 0.582 10.367 23742 Z= 0.296 Chirality : 0.044 0.156 2533 Planarity : 0.004 0.049 3097 Dihedral : 4.614 53.325 2378 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.38 % Allowed : 21.29 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: 0.01 (0.17), residues: 2162 helix: 1.87 (0.27), residues: 381 sheet: 0.82 (0.24), residues: 427 loop : -0.85 (0.15), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 75 TYR 0.018 0.001 TYR F 159 PHE 0.014 0.001 PHE F 9 TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00424 (17466) covalent geometry : angle 0.57318 (23694) SS BOND : bond 0.00519 ( 24) SS BOND : angle 2.32028 ( 48) hydrogen bonds : bond 0.03966 ( 664) hydrogen bonds : angle 4.72354 ( 1797) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 375 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: B 22 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: B 98 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8438 (tp) REVERT: B 143 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8323 (mmmm) REVERT: C 123 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7857 (tttt) REVERT: D 11 GLU cc_start: 0.7565 (mp0) cc_final: 0.6931 (mp0) REVERT: D 72 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7794 (mtmt) REVERT: D 135 ASN cc_start: 0.7658 (t0) cc_final: 0.6911 (t0) REVERT: D 161 LYS cc_start: 0.8559 (tttt) cc_final: 0.8278 (ttpt) REVERT: E 53 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7983 (mp) REVERT: E 81 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7108 (mtm110) REVERT: E 149 LYS cc_start: 0.8248 (mmmm) cc_final: 0.8021 (mmmm) REVERT: E 157 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8080 (ttmm) REVERT: F 19 ASP cc_start: 0.8265 (p0) cc_final: 0.8027 (p0) REVERT: F 58 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8638 (tptt) REVERT: H 32 ASN cc_start: 0.8586 (m-40) cc_final: 0.8365 (m110) REVERT: M 11 LEU cc_start: 0.9086 (tp) cc_final: 0.8881 (tm) outliers start: 63 outliers final: 42 residues processed: 401 average time/residue: 0.7661 time to fit residues: 334.3658 Evaluate side-chains 425 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 375 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 12 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 75 optimal weight: 0.9990 chunk 202 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 164 optimal weight: 0.5980 chunk 26 optimal weight: 0.0060 chunk 197 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 298 HIS ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 125 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 95 ASN D 125 GLN D 154 ASN E 48 ASN E 269 ASN E 271 ASN F 95 ASN F 125 GLN H 81 GLN N 37 GLN N 93 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.116130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.107760 restraints weight = 23611.671| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.52 r_work: 0.3443 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17490 Z= 0.147 Angle : 0.570 9.676 23742 Z= 0.294 Chirality : 0.044 0.183 2533 Planarity : 0.004 0.048 3097 Dihedral : 4.564 52.918 2378 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.11 % Allowed : 21.82 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: 0.03 (0.17), residues: 2162 helix: 1.80 (0.27), residues: 384 sheet: 0.82 (0.24), residues: 427 loop : -0.81 (0.15), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 75 TYR 0.019 0.001 TYR F 159 PHE 0.013 0.001 PHE D 9 TRP 0.009 0.001 TRP M 47 HIS 0.004 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00344 (17466) covalent geometry : angle 0.56120 (23694) SS BOND : bond 0.00473 ( 24) SS BOND : angle 2.27757 ( 48) hydrogen bonds : bond 0.03864 ( 664) hydrogen bonds : angle 4.69551 ( 1797) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 372 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: B 22 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8349 (m-80) REVERT: B 71 ASN cc_start: 0.8234 (p0) cc_final: 0.8029 (p0) REVERT: B 98 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8419 (tp) REVERT: B 143 LYS cc_start: 0.8600 (mmmm) cc_final: 0.8322 (mmmm) REVERT: C 123 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7833 (tttt) REVERT: D 11 GLU cc_start: 0.7570 (mp0) cc_final: 0.6935 (mp0) REVERT: D 72 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7766 (mtmt) REVERT: D 135 ASN cc_start: 0.7646 (t0) cc_final: 0.6902 (t0) REVERT: D 161 LYS cc_start: 0.8549 (tttt) cc_final: 0.8267 (ttpt) REVERT: E 53 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7988 (mp) REVERT: E 81 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7105 (mtm110) REVERT: E 157 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8096 (ttmm) REVERT: E 222 LYS cc_start: 0.8741 (ttmt) cc_final: 0.8536 (ttmm) REVERT: F 19 ASP cc_start: 0.8254 (p0) cc_final: 0.8042 (p0) REVERT: F 58 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8630 (tptt) REVERT: H 32 ASN cc_start: 0.8595 (m-40) cc_final: 0.8372 (m110) outliers start: 58 outliers final: 39 residues processed: 395 average time/residue: 0.7905 time to fit residues: 339.7318 Evaluate side-chains 412 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 365 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 12 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 54 optimal weight: 0.9990 chunk 141 optimal weight: 0.1980 chunk 206 optimal weight: 0.0070 chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 298 HIS ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 125 GLN D 28 ASN D 50 ASN D 95 ASN D 125 GLN E 269 ASN F 95 ASN F 125 GLN H 39 GLN H 81 GLN N 37 GLN N 93 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.116006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.107656 restraints weight = 23685.285| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.52 r_work: 0.3440 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17490 Z= 0.160 Angle : 0.577 12.189 23742 Z= 0.294 Chirality : 0.044 0.187 2533 Planarity : 0.004 0.049 3097 Dihedral : 4.553 52.651 2378 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.32 % Allowed : 21.66 % Favored : 75.01 % 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 are not related in a simple way. whole: 0.01 (0.17), residues: 2162 helix: 1.79 (0.27), residues: 381 sheet: 0.83 (0.24), residues: 427 loop : -0.82 (0.15), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 75 TYR 0.019 0.001 TYR F 159 PHE 0.013 0.001 PHE D 9 TRP 0.009 0.001 TRP M 47 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00375 (17466) covalent geometry : angle 0.56861 (23694) SS BOND : bond 0.00479 ( 24) SS BOND : angle 2.23963 ( 48) hydrogen bonds : bond 0.03886 ( 664) hydrogen bonds : angle 4.69236 ( 1797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7521.08 seconds wall clock time: 128 minutes 37.59 seconds (7717.59 seconds total)