Starting phenix.real_space_refine on Thu Feb 5 11:27:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mtl_48613/02_2026/9mtl_48613.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mtl_48613/02_2026/9mtl_48613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mtl_48613/02_2026/9mtl_48613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mtl_48613/02_2026/9mtl_48613.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mtl_48613/02_2026/9mtl_48613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mtl_48613/02_2026/9mtl_48613.map" } resolution = 2.41 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= 0.018 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 75 5.16 5 C 10577 2.51 5 N 2882 2.21 5 O 3237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 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: 16771 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2490 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 19, 'TRANS': 297} Chain breaks: 1 Chain: "C" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2509 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 300} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2487 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 299} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 924 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "I" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 924 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "J" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "M" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 924 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "B" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1369 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain: "D" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1369 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain: "F" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1369 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 1, 'TRANS': 167} Time building chain proxies: 3.90, per 1000 atoms: 0.23 Number of scatterers: 16771 At special positions: 0 Unit cell: (132.25, 121.67, 149.178, 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 75 16.00 O 3237 8.00 N 2882 7.00 C 10577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 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=2.04 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 C 14 " - pdb=" SG CYS D 137 " distance=2.05 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 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 E 14 " - pdb=" SG CYS F 137 " distance=2.05 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=2.03 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 H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 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 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " 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: 1.44 Conformation dependent library (CDL) restraints added in 785.8 milliseconds 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3916 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 51 sheets defined 21.6% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 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 122 through 127 removed outlier: 4.509A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 removed outlier: 4.340A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.584A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 77 removed outlier: 4.259A pdb=" N GLU E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.643A pdb=" N THR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.654A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.829A pdb=" N THR I 87 " --> pdb=" O THR I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 49 through 53 removed outlier: 3.617A pdb=" N ASN J 52 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER J 53 " --> pdb=" O ASN J 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 49 through 53' Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.918A pdb=" N GLU J 83 " --> pdb=" O THR J 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.514A pdb=" N GLU L 83 " --> pdb=" O THR L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.557A pdb=" N THR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.870A 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: 3.969A pdb=" N GLU N 83 " --> pdb=" O THR N 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 57 Processing helix chain 'B' and resid 74 through 127 removed outlier: 3.502A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.595A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 57 Processing helix chain 'D' and resid 74 through 127 removed outlier: 3.560A 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 158 through 170 removed outlier: 3.632A pdb=" N TYR D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLU D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 57 Processing helix chain 'F' and resid 74 through 127 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 170 removed outlier: 3.626A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 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: 6.456A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.534A 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 117 through 121A removed outlier: 6.651A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 117 through 121A removed outlier: 6.651A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.702A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 286 through 288 removed outlier: 3.948A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 32 through 36 Processing sheet with id=AB3, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB5, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.619A pdb=" N GLU C 44 " --> pdb=" O PHE C 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.609A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 115 through 121A removed outlier: 3.736A pdb=" N SER C 117 " --> pdb=" O GLU C 260A" (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.761A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC1, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC2, first strand: chain 'C' and resid 286 through 288 removed outlier: 3.956A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 32 through 36 Processing sheet with id=AC4, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AC5, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC6, first strand: chain 'E' and resid 43 through 44 removed outlier: 3.535A pdb=" N GLU E 44 " --> pdb=" O PHE E 294 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.666A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 115 through 121A removed outlier: 3.785A pdb=" N SER E 117 " --> pdb=" O GLU E 260A" (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU E 175 " --> pdb=" O MET E 260 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 115 through 121A removed outlier: 3.785A pdb=" N SER E 117 " --> pdb=" O GLU E 260A" (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU E 175 " --> pdb=" O MET E 260 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.260A pdb=" N ALA E 138 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ALA E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD3, first strand: chain 'E' and resid 286 through 288 removed outlier: 3.868A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.318A pdb=" N GLY H 10 " --> pdb=" O VAL H 110 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.318A pdb=" N GLY H 10 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 96 through 97 Processing sheet with id=AD8, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.647A pdb=" N ILE I 34 " --> pdb=" O SER I 50 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AE2, first strand: chain 'I' and resid 96 through 97 Processing sheet with id=AE3, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AE4, first strand: chain 'J' and resid 8 through 13 removed outlier: 6.533A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 8 through 13 Processing sheet with id=AE6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AE7, first strand: chain 'L' and resid 8 through 13 removed outlier: 6.524A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 8 through 13 Processing sheet with id=AE9, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.191A pdb=" N GLY M 10 " --> pdb=" O VAL M 110 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE M 34 " --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.191A pdb=" N GLY M 10 " --> pdb=" O VAL M 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 96 through 97 Processing sheet with id=AF4, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AF5, first strand: chain 'N' and resid 8 through 13 removed outlier: 6.605A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 8 through 13 737 hydrogen bonds defined for protein. 1920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 1.94 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: 5504 1.35 - 1.48: 4375 1.48 - 1.60: 7180 1.60 - 1.73: 0 1.73 - 1.86: 102 Bond restraints: 17161 Sorted by residual: bond pdb=" C ALA A 81A" pdb=" N ARG A 82 " ideal model delta sigma weight residual 1.333 1.496 -0.163 1.49e-02 4.50e+03 1.20e+02 bond pdb=" C PRO L 44 " pdb=" N ARG L 45 " ideal model delta sigma weight residual 1.331 1.446 -0.115 1.38e-02 5.25e+03 6.93e+01 bond pdb=" C ARG L 45 " pdb=" N LEU L 46 " ideal model delta sigma weight residual 1.331 1.413 -0.083 1.42e-02 4.96e+03 3.40e+01 bond pdb=" C ARG A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 1.331 1.265 0.066 1.26e-02 6.30e+03 2.73e+01 bond pdb=" C LYS C 211 " pdb=" N LYS C 212 " ideal model delta sigma weight residual 1.330 1.275 0.054 1.32e-02 5.74e+03 1.69e+01 ... (remaining 17156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 22689 2.09 - 4.18: 528 4.18 - 6.27: 65 6.27 - 8.36: 7 8.36 - 10.46: 6 Bond angle restraints: 23295 Sorted by residual: angle pdb=" CA PHE D 9 " pdb=" CB PHE D 9 " pdb=" CG PHE D 9 " ideal model delta sigma weight residual 113.80 122.59 -8.79 1.00e+00 1.00e+00 7.73e+01 angle pdb=" C ASP E 271 " pdb=" N THR E 272 " pdb=" CA THR E 272 " ideal model delta sigma weight residual 120.39 129.51 -9.12 1.39e+00 5.18e-01 4.31e+01 angle pdb=" N GLY D 136 " pdb=" CA GLY D 136 " pdb=" C GLY D 136 " ideal model delta sigma weight residual 115.63 106.70 8.93 1.49e+00 4.50e-01 3.59e+01 angle pdb=" CA PHE D 138 " pdb=" CB PHE D 138 " pdb=" CG PHE D 138 " ideal model delta sigma weight residual 113.80 119.05 -5.25 1.00e+00 1.00e+00 2.76e+01 angle pdb=" C ALA A 81A" pdb=" N ARG A 82 " pdb=" CA ARG A 82 " ideal model delta sigma weight residual 121.58 111.76 9.82 1.95e+00 2.63e-01 2.54e+01 ... (remaining 23290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 8842 17.64 - 35.28: 994 35.28 - 52.92: 248 52.92 - 70.56: 50 70.56 - 88.20: 23 Dihedral angle restraints: 10157 sinusoidal: 4004 harmonic: 6153 Sorted by residual: dihedral pdb=" CB CYS A 52 " pdb=" SG CYS A 52 " pdb=" SG CYS A 277 " pdb=" CB CYS A 277 " ideal model delta sinusoidal sigma weight residual -86.00 -17.94 -68.06 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual -86.00 -26.26 -59.74 1 1.00e+01 1.00e-02 4.76e+01 dihedral pdb=" CB CYS E 52 " pdb=" SG CYS E 52 " pdb=" SG CYS E 277 " pdb=" CB CYS E 277 " ideal model delta sinusoidal sigma weight residual -86.00 -31.31 -54.69 1 1.00e+01 1.00e-02 4.05e+01 ... (remaining 10154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1995 0.053 - 0.105: 446 0.105 - 0.158: 87 0.158 - 0.210: 8 0.210 - 0.263: 5 Chirality restraints: 2541 Sorted by residual: chirality pdb=" CA PHE F 138 " pdb=" N PHE F 138 " pdb=" C PHE F 138 " pdb=" CB PHE F 138 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PHE D 9 " pdb=" N PHE D 9 " pdb=" C PHE D 9 " pdb=" CB PHE D 9 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA PHE D 138 " pdb=" N PHE D 138 " pdb=" C PHE D 138 " pdb=" CB PHE D 138 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 2538 not shown) Planarity restraints: 3020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 45 " -0.751 9.50e-02 1.11e+02 3.37e-01 6.91e+01 pdb=" NE ARG L 45 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG L 45 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG L 45 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG L 45 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 82 " -0.631 9.50e-02 1.11e+02 2.83e-01 4.88e+01 pdb=" NE ARG A 82 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 82 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 82 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 82 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 261 " 0.372 9.50e-02 1.11e+02 1.67e-01 1.71e+01 pdb=" NE ARG C 261 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 261 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 261 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 261 " 0.014 2.00e-02 2.50e+03 ... (remaining 3017 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2498 2.76 - 3.29: 14871 3.29 - 3.83: 27989 3.83 - 4.36: 33823 4.36 - 4.90: 60074 Nonbonded interactions: 139255 Sorted by model distance: nonbonded pdb=" OD1 ASN F 128 " pdb=" OH TYR F 159 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASN D 128 " pdb=" OH TYR D 159 " model vdw 2.227 3.040 nonbonded pdb=" O TYR F 159 " pdb=" OG SER F 163 " model vdw 2.243 3.040 nonbonded pdb=" NZ LYS A 32 " pdb=" OD1 ASN D 50 " model vdw 2.252 3.120 nonbonded pdb=" OE1 GLU E 175 " pdb=" NH2 ARG E 261 " model vdw 2.268 3.120 ... (remaining 139250 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 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 53A or (resid 54 and (name N or na \ me CA or name C or name O or name CB )) or resid 55 through 309 or (resid 310 an \ d (name N or name CA or name C or name O or name CB )) or resid 311 through 324) \ ) selection = (chain 'C' and (resid 11 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 53A or (resid 54 and (name N or na \ me CA or name C or name O or name CB )) or resid 55 through 76 or resid 81A thro \ ugh 324)) selection = (chain 'E' and (resid 11 through 76 or resid 81A through 324)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'L' 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.050 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 0.163 17184 Z= 0.281 Angle : 0.750 10.455 23341 Z= 0.456 Chirality : 0.047 0.263 2541 Planarity : 0.010 0.337 3020 Dihedral : 16.050 88.195 6172 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.99 % Rotamer: Outliers : 1.64 % Allowed : 18.37 % Favored : 79.99 % Cbeta Deviations : 0.05 % 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: 0.18 (0.17), residues: 2123 helix: 2.21 (0.27), residues: 348 sheet: 0.75 (0.24), residues: 481 loop : -0.75 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 123 TYR 0.013 0.002 TYR J 91 PHE 0.021 0.002 PHE D 9 TRP 0.008 0.001 TRP F 21 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00516 (17161) covalent geometry : angle 0.74546 (23295) SS BOND : bond 0.00683 ( 23) SS BOND : angle 1.97381 ( 46) hydrogen bonds : bond 0.11431 ( 691) hydrogen bonds : angle 6.16305 ( 1920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 427 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: A 230 MET cc_start: 0.8689 (ttm) cc_final: 0.8480 (ttp) REVERT: C 106 GLU cc_start: 0.7741 (mp0) cc_final: 0.7477 (mp0) REVERT: I 37 VAL cc_start: 0.8579 (p) cc_final: 0.8364 (p) REVERT: I 96 ARG cc_start: 0.8789 (ttt90) cc_final: 0.8530 (ttt90) REVERT: B 119 TYR cc_start: 0.8707 (t80) cc_final: 0.8430 (t80) REVERT: B 141 TYR cc_start: 0.8551 (m-80) cc_final: 0.8323 (m-80) REVERT: D 119 TYR cc_start: 0.8732 (t80) cc_final: 0.8412 (t80) REVERT: F 59 MET cc_start: 0.7803 (mmm) cc_final: 0.7584 (tpp) outliers start: 30 outliers final: 17 residues processed: 443 average time/residue: 0.8241 time to fit residues: 396.3940 Evaluate side-chains 439 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 421 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain F residue 19 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 ASN B 154 ASN B 169 ASN D 125 GLN D 154 ASN D 169 ASN F 28 ASN F 50 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.113265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.105635 restraints weight = 23342.628| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.34 r_work: 0.3450 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17184 Z= 0.215 Angle : 0.584 9.801 23341 Z= 0.308 Chirality : 0.045 0.147 2541 Planarity : 0.004 0.058 3020 Dihedral : 5.761 58.867 2354 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.06 % Allowed : 16.61 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.17), residues: 2123 helix: 2.35 (0.27), residues: 351 sheet: 0.94 (0.24), residues: 471 loop : -0.74 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 123 TYR 0.014 0.002 TYR I 91 PHE 0.018 0.002 PHE D 9 TRP 0.007 0.001 TRP J 35 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00514 (17161) covalent geometry : angle 0.58198 (23295) SS BOND : bond 0.00302 ( 23) SS BOND : angle 1.34879 ( 46) hydrogen bonds : bond 0.04603 ( 691) hydrogen bonds : angle 4.95837 ( 1920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 415 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8196 (mtmt) REVERT: C 192 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: E 31 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7630 (mm-30) REVERT: J 97 ARG cc_start: 0.8384 (tpp-160) cc_final: 0.8005 (mmt-90) REVERT: B 97 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: B 119 TYR cc_start: 0.8657 (t80) cc_final: 0.8365 (t80) REVERT: D 119 TYR cc_start: 0.8660 (t80) cc_final: 0.8355 (t80) REVERT: F 17 MET cc_start: 0.8649 (ttp) cc_final: 0.8256 (ttp) REVERT: F 59 MET cc_start: 0.7765 (mmm) cc_final: 0.7543 (tpp) outliers start: 74 outliers final: 35 residues processed: 452 average time/residue: 0.7100 time to fit residues: 350.3009 Evaluate side-chains 449 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 411 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain N residue 103 HIS Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 149 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 65 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 67 optimal weight: 0.0870 chunk 114 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN E 165 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 169 ASN D 125 GLN D 154 ASN D 169 ASN F 28 ASN F 72 HIS F 114 ASN F 154 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.112992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.105562 restraints weight = 24108.212| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.34 r_work: 0.3457 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17184 Z= 0.177 Angle : 0.553 8.825 23341 Z= 0.292 Chirality : 0.044 0.146 2541 Planarity : 0.004 0.058 3020 Dihedral : 5.138 53.603 2334 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.84 % Allowed : 17.98 % Favored : 78.18 % 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: 0.33 (0.17), residues: 2123 helix: 2.47 (0.27), residues: 349 sheet: 0.86 (0.23), residues: 491 loop : -0.71 (0.16), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 123 TYR 0.014 0.001 TYR I 91 PHE 0.013 0.001 PHE D 9 TRP 0.007 0.001 TRP J 35 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00421 (17161) covalent geometry : angle 0.55013 (23295) SS BOND : bond 0.00246 ( 23) SS BOND : angle 1.30459 ( 46) hydrogen bonds : bond 0.04369 ( 691) hydrogen bonds : angle 4.79558 ( 1920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 417 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8197 (mtmt) REVERT: A 211 LYS cc_start: 0.8317 (ttmm) cc_final: 0.8100 (ttmt) REVERT: C 106 GLU cc_start: 0.7688 (mp0) cc_final: 0.7436 (mp0) REVERT: C 192 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: E 82 ARG cc_start: 0.8372 (mmt-90) cc_final: 0.8117 (mpt180) REVERT: I 82 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8108 (mtt) REVERT: J 97 ARG cc_start: 0.8398 (tpp-160) cc_final: 0.8018 (mmt-90) REVERT: B 97 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: B 119 TYR cc_start: 0.8648 (t80) cc_final: 0.8370 (t80) REVERT: D 103 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7261 (mm-30) REVERT: D 119 TYR cc_start: 0.8648 (t80) cc_final: 0.8331 (t80) REVERT: F 17 MET cc_start: 0.8654 (ttp) cc_final: 0.8307 (ttp) REVERT: F 59 MET cc_start: 0.7755 (mmm) cc_final: 0.7529 (tpp) REVERT: F 68 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8444 (mttp) outliers start: 70 outliers final: 35 residues processed: 450 average time/residue: 0.7075 time to fit residues: 347.2334 Evaluate side-chains 451 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 411 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain N residue 103 HIS Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 22 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 0.0870 chunk 119 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN C 295 GLN E 165 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 169 ASN D 125 GLN D 154 ASN F 28 ASN F 72 HIS F 154 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.112038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.104791 restraints weight = 24054.519| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.30 r_work: 0.3447 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17184 Z= 0.223 Angle : 0.577 9.722 23341 Z= 0.304 Chirality : 0.046 0.227 2541 Planarity : 0.004 0.059 3020 Dihedral : 5.080 48.196 2332 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.33 % Allowed : 17.98 % Favored : 77.69 % 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: 0.24 (0.17), residues: 2123 helix: 2.38 (0.26), residues: 349 sheet: 0.87 (0.24), residues: 466 loop : -0.77 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 123 TYR 0.022 0.002 TYR E 201 PHE 0.015 0.002 PHE D 9 TRP 0.008 0.001 TRP J 35 HIS 0.005 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00534 (17161) covalent geometry : angle 0.57302 (23295) SS BOND : bond 0.00389 ( 23) SS BOND : angle 1.58737 ( 46) hydrogen bonds : bond 0.04493 ( 691) hydrogen bonds : angle 4.79011 ( 1920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 408 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8197 (mtmt) REVERT: A 224 ARG cc_start: 0.8546 (mtt-85) cc_final: 0.8291 (mtt-85) REVERT: A 225 ASP cc_start: 0.7790 (t0) cc_final: 0.7493 (t0) REVERT: C 106 GLU cc_start: 0.7703 (mp0) cc_final: 0.7445 (mp0) REVERT: C 192 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: J 97 ARG cc_start: 0.8407 (tpp-160) cc_final: 0.8035 (mmt-90) REVERT: L 45 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8305 (ttt180) REVERT: B 97 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: B 119 TYR cc_start: 0.8649 (t80) cc_final: 0.8353 (t80) REVERT: D 103 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7223 (mm-30) REVERT: D 119 TYR cc_start: 0.8663 (t80) cc_final: 0.8366 (t80) REVERT: F 17 MET cc_start: 0.8646 (ttp) cc_final: 0.8393 (ttp) REVERT: F 59 MET cc_start: 0.7763 (mmm) cc_final: 0.7530 (tpp) REVERT: F 68 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8485 (mttp) REVERT: F 74 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7538 (mt-10) outliers start: 79 outliers final: 35 residues processed: 453 average time/residue: 0.7664 time to fit residues: 378.6941 Evaluate side-chains 445 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 405 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 103 HIS Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 105 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 59 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 67 optimal weight: 0.0270 chunk 164 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN C 295 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 169 ASN D 125 GLN D 154 ASN F 28 ASN F 72 HIS F 125 GLN F 154 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.112585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.105389 restraints weight = 23892.846| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.29 r_work: 0.3455 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17184 Z= 0.175 Angle : 0.556 10.271 23341 Z= 0.293 Chirality : 0.045 0.218 2541 Planarity : 0.004 0.059 3020 Dihedral : 4.815 41.823 2326 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.51 % Allowed : 18.53 % Favored : 77.96 % 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: 0.31 (0.17), residues: 2123 helix: 2.48 (0.27), residues: 349 sheet: 0.87 (0.24), residues: 486 loop : -0.74 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 123 TYR 0.014 0.001 TYR I 91 PHE 0.012 0.001 PHE D 9 TRP 0.007 0.001 TRP M 36 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00418 (17161) covalent geometry : angle 0.55147 (23295) SS BOND : bond 0.00382 ( 23) SS BOND : angle 1.64514 ( 46) hydrogen bonds : bond 0.04277 ( 691) hydrogen bonds : angle 4.72321 ( 1920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 413 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 225 ASP cc_start: 0.7745 (t0) cc_final: 0.7441 (t0) REVERT: C 192 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: E 82 ARG cc_start: 0.8378 (mmt-90) cc_final: 0.8125 (mpt180) REVERT: J 97 ARG cc_start: 0.8409 (tpp-160) cc_final: 0.8014 (mmt-90) REVERT: L 45 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8308 (ttt180) REVERT: B 27 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7563 (tp-100) REVERT: B 97 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: B 119 TYR cc_start: 0.8632 (t80) cc_final: 0.8365 (t80) REVERT: D 103 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7211 (mm-30) REVERT: D 119 TYR cc_start: 0.8654 (t80) cc_final: 0.8358 (t80) REVERT: F 17 MET cc_start: 0.8652 (ttp) cc_final: 0.8424 (ttp) REVERT: F 59 MET cc_start: 0.7750 (mmm) cc_final: 0.7513 (tpp) REVERT: F 68 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8416 (mttp) REVERT: F 74 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7551 (mt-10) outliers start: 64 outliers final: 41 residues processed: 446 average time/residue: 0.7848 time to fit residues: 381.4651 Evaluate side-chains 460 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 414 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 103 HIS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 105 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 91 optimal weight: 0.2980 chunk 183 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN C 295 GLN E 183 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 169 ASN D 125 GLN D 154 ASN F 28 ASN F 72 HIS F 125 GLN F 154 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.112080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.104890 restraints weight = 23903.897| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.29 r_work: 0.3445 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17184 Z= 0.216 Angle : 0.579 11.163 23341 Z= 0.304 Chirality : 0.046 0.228 2541 Planarity : 0.004 0.059 3020 Dihedral : 4.874 41.955 2326 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.95 % Allowed : 19.41 % Favored : 76.64 % 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: 0.23 (0.17), residues: 2123 helix: 2.38 (0.26), residues: 349 sheet: 0.87 (0.24), residues: 466 loop : -0.78 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 123 TYR 0.014 0.002 TYR I 91 PHE 0.014 0.001 PHE D 9 TRP 0.008 0.001 TRP N 35 HIS 0.005 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00518 (17161) covalent geometry : angle 0.57406 (23295) SS BOND : bond 0.00431 ( 23) SS BOND : angle 1.79026 ( 46) hydrogen bonds : bond 0.04423 ( 691) hydrogen bonds : angle 4.74764 ( 1920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 409 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8075 (mp) REVERT: A 224 ARG cc_start: 0.8532 (mtt-85) cc_final: 0.8252 (mtt-85) REVERT: A 225 ASP cc_start: 0.7779 (t0) cc_final: 0.7483 (t0) REVERT: C 106 GLU cc_start: 0.7699 (mp0) cc_final: 0.7449 (mp0) REVERT: C 192 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: J 97 ARG cc_start: 0.8431 (tpp-160) cc_final: 0.8027 (mmt-90) REVERT: L 45 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8316 (ttt180) REVERT: B 27 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7516 (tp-100) REVERT: B 97 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: B 119 TYR cc_start: 0.8649 (t80) cc_final: 0.8374 (t80) REVERT: D 119 TYR cc_start: 0.8676 (t80) cc_final: 0.8326 (t80) REVERT: F 59 MET cc_start: 0.7763 (mmm) cc_final: 0.7522 (tpp) REVERT: F 68 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8422 (mttp) REVERT: F 74 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7563 (mt-10) outliers start: 72 outliers final: 42 residues processed: 445 average time/residue: 0.7802 time to fit residues: 377.9055 Evaluate side-chains 454 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 406 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 103 HIS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 105 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 105 optimal weight: 0.7980 chunk 130 optimal weight: 0.1980 chunk 201 optimal weight: 0.5980 chunk 133 optimal weight: 0.0570 chunk 52 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 94 optimal weight: 0.0970 chunk 203 optimal weight: 1.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN C 295 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 169 ASN D 125 GLN D 154 ASN F 28 ASN F 62 GLN F 72 HIS F 125 GLN F 154 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.114561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.106866 restraints weight = 23051.955| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.36 r_work: 0.3470 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17184 Z= 0.118 Angle : 0.541 12.444 23341 Z= 0.284 Chirality : 0.044 0.310 2541 Planarity : 0.004 0.059 3020 Dihedral : 4.592 44.725 2326 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.23 % Allowed : 20.07 % Favored : 76.70 % 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: 0.49 (0.17), residues: 2123 helix: 2.61 (0.27), residues: 349 sheet: 1.24 (0.25), residues: 438 loop : -0.65 (0.15), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 123 TYR 0.009 0.001 TYR I 91 PHE 0.010 0.001 PHE F 9 TRP 0.009 0.001 TRP E 84 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00277 (17161) covalent geometry : angle 0.53465 (23295) SS BOND : bond 0.00619 ( 23) SS BOND : angle 1.92428 ( 46) hydrogen bonds : bond 0.03921 ( 691) hydrogen bonds : angle 4.57340 ( 1920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 414 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 225 ASP cc_start: 0.7721 (t0) cc_final: 0.7423 (t0) REVERT: C 106 GLU cc_start: 0.7694 (mp0) cc_final: 0.7441 (mp0) REVERT: C 192 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: E 82 ARG cc_start: 0.8386 (mmt-90) cc_final: 0.8137 (mpt180) REVERT: E 106 GLU cc_start: 0.7688 (mp0) cc_final: 0.7446 (mp0) REVERT: B 97 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: B 119 TYR cc_start: 0.8589 (t80) cc_final: 0.8310 (t80) REVERT: D 119 TYR cc_start: 0.8634 (t80) cc_final: 0.8320 (t80) REVERT: F 74 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7469 (mt-10) outliers start: 59 outliers final: 35 residues processed: 445 average time/residue: 0.7859 time to fit residues: 380.9001 Evaluate side-chains 443 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 406 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 103 HIS Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 105 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 0.0070 chunk 127 optimal weight: 0.8980 chunk 12 optimal weight: 0.0570 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN C 275 HIS C 295 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 169 ASN D 125 GLN D 154 ASN F 28 ASN F 62 GLN F 72 HIS F 154 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.113763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.106126 restraints weight = 23316.451| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.34 r_work: 0.3459 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17184 Z= 0.164 Angle : 0.568 13.115 23341 Z= 0.296 Chirality : 0.045 0.286 2541 Planarity : 0.004 0.058 3020 Dihedral : 4.614 44.130 2325 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.02 % Allowed : 20.45 % Favored : 76.54 % 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: 0.42 (0.17), residues: 2123 helix: 2.55 (0.26), residues: 349 sheet: 0.99 (0.24), residues: 471 loop : -0.65 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 123 TYR 0.011 0.001 TYR I 91 PHE 0.012 0.001 PHE D 9 TRP 0.008 0.001 TRP E 84 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00395 (17161) covalent geometry : angle 0.56108 (23295) SS BOND : bond 0.00622 ( 23) SS BOND : angle 2.02107 ( 46) hydrogen bonds : bond 0.04099 ( 691) hydrogen bonds : angle 4.61314 ( 1920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 405 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 225 ASP cc_start: 0.7718 (t0) cc_final: 0.7436 (t0) REVERT: C 106 GLU cc_start: 0.7666 (mp0) cc_final: 0.7431 (mp0) REVERT: C 192 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: E 82 ARG cc_start: 0.8374 (mmt-90) cc_final: 0.8127 (mpt180) REVERT: E 106 GLU cc_start: 0.7675 (mp0) cc_final: 0.7433 (mp0) REVERT: J 97 ARG cc_start: 0.8396 (tpp-160) cc_final: 0.8048 (mmt-90) REVERT: B 27 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7580 (tp-100) REVERT: B 97 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: B 119 TYR cc_start: 0.8606 (t80) cc_final: 0.8342 (t80) REVERT: D 119 TYR cc_start: 0.8596 (t80) cc_final: 0.8308 (t80) REVERT: F 74 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7469 (mt-10) outliers start: 55 outliers final: 40 residues processed: 435 average time/residue: 0.8023 time to fit residues: 379.7373 Evaluate side-chains 452 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 409 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 103 HIS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 105 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 93 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 191 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN C 295 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 169 ASN D 125 GLN D 154 ASN F 28 ASN F 50 ASN F 62 GLN F 72 HIS F 125 GLN F 154 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.112591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.105384 restraints weight = 24008.310| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.30 r_work: 0.3455 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 17184 Z= 0.188 Angle : 0.587 12.686 23341 Z= 0.306 Chirality : 0.045 0.274 2541 Planarity : 0.004 0.058 3020 Dihedral : 4.685 44.353 2325 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.07 % Allowed : 20.72 % Favored : 76.21 % 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: 0.38 (0.17), residues: 2123 helix: 2.40 (0.26), residues: 351 sheet: 0.98 (0.24), residues: 471 loop : -0.65 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 123 TYR 0.022 0.002 TYR E 201 PHE 0.019 0.001 PHE I 67 TRP 0.007 0.001 TRP N 35 HIS 0.005 0.001 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00453 (17161) covalent geometry : angle 0.58049 (23295) SS BOND : bond 0.00600 ( 23) SS BOND : angle 2.00299 ( 46) hydrogen bonds : bond 0.04242 ( 691) hydrogen bonds : angle 4.64371 ( 1920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 408 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8115 (mp) REVERT: A 225 ASP cc_start: 0.7700 (t0) cc_final: 0.7425 (t0) REVERT: C 106 GLU cc_start: 0.7657 (mp0) cc_final: 0.7411 (mp0) REVERT: C 192 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: B 27 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7551 (tp-100) REVERT: B 97 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: B 119 TYR cc_start: 0.8627 (t80) cc_final: 0.8363 (t80) REVERT: D 119 TYR cc_start: 0.8607 (t80) cc_final: 0.8273 (t80) REVERT: F 68 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8401 (mttp) REVERT: F 74 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7501 (mt-10) outliers start: 56 outliers final: 35 residues processed: 434 average time/residue: 0.8176 time to fit residues: 385.9333 Evaluate side-chains 447 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 407 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 103 HIS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 193 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 189 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN C 275 HIS C 295 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 169 ASN D 125 GLN D 154 ASN F 28 ASN F 50 ASN F 62 GLN F 72 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.112916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.105429 restraints weight = 23823.617| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.38 r_work: 0.3454 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17184 Z= 0.164 Angle : 0.590 14.539 23341 Z= 0.308 Chirality : 0.045 0.341 2541 Planarity : 0.004 0.059 3020 Dihedral : 4.649 45.396 2323 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.85 % Allowed : 21.11 % Favored : 76.04 % 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: 0.39 (0.17), residues: 2123 helix: 2.39 (0.26), residues: 351 sheet: 0.96 (0.24), residues: 471 loop : -0.63 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 123 TYR 0.011 0.001 TYR M 91 PHE 0.012 0.001 PHE D 9 TRP 0.008 0.001 TRP E 84 HIS 0.004 0.001 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00393 (17161) covalent geometry : angle 0.58121 (23295) SS BOND : bond 0.00706 ( 23) SS BOND : angle 2.30968 ( 46) hydrogen bonds : bond 0.04149 ( 691) hydrogen bonds : angle 4.63163 ( 1920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 403 time to evaluate : 0.535 Fit side-chains REVERT: A 42 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8151 (mp) REVERT: A 225 ASP cc_start: 0.7731 (t0) cc_final: 0.7450 (t0) REVERT: C 106 GLU cc_start: 0.7717 (mp0) cc_final: 0.7475 (mp0) REVERT: C 192 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: J 97 ARG cc_start: 0.8427 (tpp-160) cc_final: 0.8055 (mmt-90) REVERT: B 27 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7592 (tp-100) REVERT: B 97 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: B 119 TYR cc_start: 0.8630 (t80) cc_final: 0.8355 (t80) REVERT: D 119 TYR cc_start: 0.8622 (t80) cc_final: 0.8320 (t80) REVERT: F 68 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8412 (mttp) REVERT: F 74 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7508 (mt-10) outliers start: 52 outliers final: 35 residues processed: 432 average time/residue: 0.7319 time to fit residues: 344.4095 Evaluate side-chains 439 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 399 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 103 HIS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 207 optimal weight: 0.0870 chunk 86 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN C 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 169 ASN D 125 GLN D 154 ASN F 28 ASN F 50 ASN F 62 GLN F 72 HIS F 125 GLN F 154 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.112522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.105040 restraints weight = 23874.114| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.37 r_work: 0.3447 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 17184 Z= 0.191 Angle : 0.610 15.365 23341 Z= 0.317 Chirality : 0.046 0.321 2541 Planarity : 0.004 0.060 3020 Dihedral : 4.712 45.600 2323 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.63 % Allowed : 21.33 % Favored : 76.04 % 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: 0.36 (0.17), residues: 2123 helix: 2.36 (0.26), residues: 351 sheet: 0.98 (0.24), residues: 476 loop : -0.68 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 123 TYR 0.012 0.001 TYR M 91 PHE 0.026 0.002 PHE H 67 TRP 0.007 0.001 TRP J 35 HIS 0.004 0.001 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00460 (17161) covalent geometry : angle 0.60170 (23295) SS BOND : bond 0.00720 ( 23) SS BOND : angle 2.38547 ( 46) hydrogen bonds : bond 0.04267 ( 691) hydrogen bonds : angle 4.65731 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7894.66 seconds wall clock time: 135 minutes 0.67 seconds (8100.67 seconds total)