Starting phenix.real_space_refine on Thu Feb 5 11:18:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mtm_48614/02_2026/9mtm_48614.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mtm_48614/02_2026/9mtm_48614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mtm_48614/02_2026/9mtm_48614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mtm_48614/02_2026/9mtm_48614.map" model { file = "/net/cci-nas-00/data/ceres_data/9mtm_48614/02_2026/9mtm_48614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mtm_48614/02_2026/9mtm_48614.cif" } resolution = 2.49 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 78 5.16 5 C 10543 2.51 5 N 2880 2.21 5 O 3261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16762 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2513 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 19, 'TRANS': 300} Chain breaks: 1 Chain: "C" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2513 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 19, 'TRANS': 300} Chain breaks: 1 Chain: "E" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 300} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 947 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "I" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 947 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "J" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 766 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "L" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 766 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "M" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 938 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "N" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 766 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "B" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1365 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 167} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 3.37, per 1000 atoms: 0.20 Number of scatterers: 16762 At special positions: 0 Unit cell: (148.12, 137.54, 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 78 16.00 O 3261 8.00 N 2880 7.00 C 10543 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.04 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.04 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.08 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=2.07 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: 1.22 Conformation dependent library (CDL) restraints added in 713.7 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: 3922 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 45 sheets defined 20.2% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 removed outlier: 4.162A 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 187 through 195 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 77 removed outlier: 4.144A 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 195 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.709A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.736A 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 79 through 83 removed outlier: 3.582A pdb=" N ASP J 82 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 79 through 83' Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.811A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.709A 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: 3.672A pdb=" N ASP N 82 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 79 through 83' Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 74 through 127 removed outlier: 3.575A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.863A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 127 removed outlier: 3.558A 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 162 through 170 Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 74 through 127 removed outlier: 3.530A pdb=" N GLU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 162 through 170 Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 61 removed outlier: 6.398A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 115 through 121 removed outlier: 7.851A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 121 Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.824A 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 287 through 288 removed outlier: 3.781A 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 Processing sheet with id=AB6, first strand: chain 'C' and resid 59 through 61 removed outlier: 6.320A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.465A 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 121 Processing sheet with id=AB8, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.633A pdb=" N ALA C 138 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N ALA C 144 " --> pdb=" O ALA C 138 " (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: 3.615A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 64 " --> pdb=" O GLY C 303 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 31 through 36 removed outlier: 3.524A pdb=" N GLY F 31 " --> pdb=" O ASN F 28 " (cutoff:3.500A) 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 Processing sheet with id=AC7, first strand: chain 'E' and resid 59 through 61 removed outlier: 6.333A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 115 through 121A removed outlier: 6.236A pdb=" N GLU E 260A" --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE E 118 " --> pdb=" O THR E 259 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR E 259 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG E 120 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA E 257 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU E 175 " --> pdb=" O MET E 260 " (cutoff:3.500A) removed outlier: 7.926A 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: 6.236A pdb=" N GLU E 260A" --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE E 118 " --> pdb=" O THR E 259 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR E 259 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG E 120 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA E 257 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.653A 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: 7.752A pdb=" N ALA E 138 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 10.736A 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: 3.609A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR F 64 " --> pdb=" O GLY E 303 " (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 11 removed outlier: 6.348A pdb=" N GLY H 10 " --> pdb=" O VAL H 110 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N TYR H 32 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TYR H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.630A 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 11 removed outlier: 6.348A pdb=" N GLY H 10 " --> pdb=" O VAL H 110 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL H 96 " --> pdb=" O MET H 100F" (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET H 100F" --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N VAL H 98 " --> pdb=" O MET H 100D" (cutoff:3.500A) removed outlier: 9.659A pdb=" N MET H 100D" --> pdb=" O VAL H 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.347A pdb=" N GLY I 10 " --> pdb=" O VAL I 110 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N TYR I 32 " --> pdb=" O TYR I 52 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TYR I 52 " --> pdb=" O TYR I 32 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.347A pdb=" N GLY I 10 " --> pdb=" O VAL I 110 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL I 96 " --> pdb=" O MET I 100F" (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET I 100F" --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 10.733A pdb=" N VAL I 98 " --> pdb=" O MET I 100D" (cutoff:3.500A) removed outlier: 9.588A pdb=" N MET I 100D" --> pdb=" O VAL I 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 3 through 5 Processing sheet with id=AE2, first strand: chain 'J' and resid 45 through 49 removed outlier: 6.499A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AE4, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.529A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.448A pdb=" N GLY M 10 " --> pdb=" O VAL M 110 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N TYR M 32 " --> pdb=" O TYR M 52 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N TYR M 52 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE M 34 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.448A pdb=" N GLY M 10 " --> pdb=" O VAL M 110 " (cutoff:3.500A) removed outlier: 11.034A pdb=" N CYS M 92 " --> pdb=" O ASP M 101 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ASP M 101 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG M 94 " --> pdb=" O ALA M 100E" (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA M 100E" --> pdb=" O ARG M 94 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL M 96 " --> pdb=" O MET M 100C" (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 3 through 5 Processing sheet with id=AE9, first strand: chain 'N' and resid 45 through 49 removed outlier: 5.584A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN N 95A" --> pdb=" O LYS N 92 " (cutoff:3.500A) 698 hydrogen bonds defined for protein. 1860 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5507 1.34 - 1.47: 4171 1.47 - 1.59: 7354 1.59 - 1.71: 0 1.71 - 1.84: 108 Bond restraints: 17140 Sorted by residual: bond pdb=" C GLU A 119 " pdb=" N ARG A 120 " ideal model delta sigma weight residual 1.330 1.254 0.076 1.32e-02 5.74e+03 3.29e+01 bond pdb=" C ASN B 71 " pdb=" N HIS B 72 " ideal model delta sigma weight residual 1.335 1.265 0.070 1.34e-02 5.57e+03 2.75e+01 bond pdb=" C LYS B 82 " pdb=" N LYS B 83 " ideal model delta sigma weight residual 1.335 1.272 0.063 1.31e-02 5.83e+03 2.28e+01 bond pdb=" C ARG A 120 " pdb=" N PHE A 121 " ideal model delta sigma weight residual 1.331 1.265 0.066 1.41e-02 5.03e+03 2.18e+01 bond pdb=" C ALA E 81A" pdb=" N ARG E 82 " ideal model delta sigma weight residual 1.333 1.263 0.070 1.55e-02 4.16e+03 2.04e+01 ... (remaining 17135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 22332 1.67 - 3.34: 711 3.34 - 5.01: 156 5.01 - 6.68: 38 6.68 - 8.35: 7 Bond angle restraints: 23244 Sorted by residual: angle pdb=" C HIS F 142 " pdb=" CA HIS F 142 " pdb=" CB HIS F 142 " ideal model delta sigma weight residual 114.40 106.05 8.35 1.25e+00 6.40e-01 4.46e+01 angle pdb=" CA PHE A 213 " pdb=" CB PHE A 213 " pdb=" CG PHE A 213 " ideal model delta sigma weight residual 113.80 119.59 -5.79 1.00e+00 1.00e+00 3.35e+01 angle pdb=" CA HIS B 142 " pdb=" CB HIS B 142 " pdb=" CG HIS B 142 " ideal model delta sigma weight residual 113.80 119.41 -5.61 1.00e+00 1.00e+00 3.15e+01 angle pdb=" N LEU E 71 " pdb=" CA LEU E 71 " pdb=" C LEU E 71 " ideal model delta sigma weight residual 113.41 107.14 6.27 1.22e+00 6.72e-01 2.64e+01 angle pdb=" CA HIS F 142 " pdb=" CB HIS F 142 " pdb=" CG HIS F 142 " ideal model delta sigma weight residual 113.80 118.49 -4.69 1.00e+00 1.00e+00 2.20e+01 ... (remaining 23239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 8744 18.08 - 36.16: 1044 36.16 - 54.24: 320 54.24 - 72.33: 63 72.33 - 90.41: 16 Dihedral angle restraints: 10187 sinusoidal: 4028 harmonic: 6159 Sorted by residual: dihedral pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " pdb=" SG CYS F 148 " pdb=" CB CYS F 148 " ideal model delta sinusoidal sigma weight residual 93.00 13.27 79.73 1 1.00e+01 1.00e-02 7.89e+01 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 -11.95 -74.05 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CD ARG E 82 " pdb=" NE ARG E 82 " pdb=" CZ ARG E 82 " pdb=" NH1 ARG E 82 " ideal model delta sinusoidal sigma weight residual 0.00 -60.55 60.55 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 10184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1929 0.053 - 0.105: 483 0.105 - 0.158: 99 0.158 - 0.210: 17 0.210 - 0.263: 3 Chirality restraints: 2531 Sorted by residual: chirality pdb=" CA LEU E 320 " pdb=" N LEU E 320 " pdb=" C LEU E 320 " pdb=" CB LEU E 320 " 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 GLU E 75 " pdb=" N GLU E 75 " pdb=" C GLU E 75 " pdb=" CB GLU E 75 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ARG A 120 " pdb=" N ARG A 120 " pdb=" C ARG A 120 " pdb=" CB ARG A 120 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2528 not shown) Planarity restraints: 3018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 82 " -0.960 9.50e-02 1.11e+02 4.30e-01 1.12e+02 pdb=" NE ARG E 82 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG E 82 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG E 82 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 82 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 321 " -0.454 9.50e-02 1.11e+02 2.04e-01 2.54e+01 pdb=" NE ARG A 321 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 321 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 321 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 321 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 120 " 0.311 9.50e-02 1.11e+02 1.40e-01 1.20e+01 pdb=" NE ARG A 120 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 120 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 120 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 120 " 0.012 2.00e-02 2.50e+03 ... (remaining 3015 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 129 2.58 - 3.16: 12950 3.16 - 3.74: 25291 3.74 - 4.32: 37515 4.32 - 4.90: 63443 Nonbonded interactions: 139328 Sorted by model distance: nonbonded pdb=" O GLN E 196 " pdb=" OD1 ASN E 197 " model vdw 1.995 3.040 nonbonded pdb=" N GLU D 11 " pdb=" OE1 GLU D 11 " model vdw 2.171 3.120 nonbonded pdb=" NH1 ARG J 61 " pdb=" OD2 ASP J 82 " model vdw 2.225 3.120 nonbonded pdb=" OD1 ASN F 128 " pdb=" OH TYR F 159 " model vdw 2.229 3.040 nonbonded pdb=" OE2 GLU H 33 " pdb=" OG SER H 35 " model vdw 2.232 3.040 ... (remaining 139323 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 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 207 or (resid 208 and (name N or n \ ame CA or name C or name O or name CB )) or resid 209 through 324)) selection = (chain 'C' and (resid 11 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 207 or (resid 208 and (name N or n \ ame CA or name C or name O or name CB )) or resid 209 through 324)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 2 through 142 or (resid 143 and (name N or name CA or name \ C or name O or name CB )) or resid 144 through 170)) selection = (chain 'F' and (resid 2 through 142 or (resid 143 and (name N or name CA or name \ C or name O or name CB )) or resid 144 through 170)) } ncs_group { reference = (chain 'H' and resid 2 through 116) selection = (chain 'I' and resid 2 through 116) 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: 2.980 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.220 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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: 0.020 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 : 0.006 0.076 17164 Z= 0.293 Angle : 0.758 14.623 23292 Z= 0.458 Chirality : 0.049 0.263 2531 Planarity : 0.011 0.430 3018 Dihedral : 17.249 90.407 6193 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.00 % Favored : 95.81 % Rotamer: Outliers : 2.45 % Allowed : 26.76 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.18), residues: 2123 helix: 2.16 (0.27), residues: 351 sheet: 0.96 (0.26), residues: 437 loop : -0.67 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 123 TYR 0.013 0.002 TYR M 32 PHE 0.020 0.002 PHE A 213 TRP 0.010 0.001 TRP F 21 HIS 0.011 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00576 (17140) covalent geometry : angle 0.73954 (23244) SS BOND : bond 0.01419 ( 24) SS BOND : angle 3.70717 ( 48) hydrogen bonds : bond 0.09000 ( 672) hydrogen bonds : angle 5.54674 ( 1860) *********************** 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 451 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 406 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 315 ARG cc_start: 0.8851 (mtp85) cc_final: 0.8603 (mtt-85) REVERT: E 132 ASP cc_start: 0.8459 (m-30) cc_final: 0.8246 (m-30) REVERT: I 82 MET cc_start: 0.8520 (mtm) cc_final: 0.8234 (mtp) REVERT: D 74 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7718 (mt-10) REVERT: D 102 LEU cc_start: 0.8383 (mt) cc_final: 0.8177 (mm) REVERT: F 170 ARG cc_start: 0.8482 (ttm110) cc_final: 0.8242 (ttp-170) outliers start: 45 outliers final: 31 residues processed: 436 average time/residue: 0.7355 time to fit residues: 347.4184 Evaluate side-chains 424 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 393 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain E residue 63 LYS Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain F residue 142 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0040 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.0370 chunk 122 optimal weight: 1.9990 overall best weight: 0.3028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 196 GLN A 231 ASN ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN E 159 ASN E 165 ASN E 278 ASN I 76 ASN J 31 ASN B 30 GLN B 71 ASN B 72 HIS B 125 GLN B 154 ASN D 43 ASN D 125 GLN F 30 GLN F 43 ASN F 95 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.110822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.103323 restraints weight = 23873.258| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.43 r_work: 0.3393 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17164 Z= 0.119 Angle : 0.508 6.105 23292 Z= 0.275 Chirality : 0.042 0.162 2531 Planarity : 0.004 0.049 3018 Dihedral : 5.644 55.257 2375 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.45 % Favored : 97.46 % Rotamer: Outliers : 4.36 % Allowed : 23.60 % Favored : 72.04 % 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: 0.49 (0.18), residues: 2123 helix: 2.58 (0.27), residues: 351 sheet: 0.75 (0.25), residues: 492 loop : -0.50 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 123 TYR 0.015 0.001 TYR E 201 PHE 0.013 0.001 PHE D 3 TRP 0.008 0.001 TRP F 21 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00269 (17140) covalent geometry : angle 0.50289 (23244) SS BOND : bond 0.00339 ( 24) SS BOND : angle 1.64913 ( 48) hydrogen bonds : bond 0.04097 ( 672) hydrogen bonds : angle 4.67175 ( 1860) *********************** 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 475 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 395 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 315 ARG cc_start: 0.8780 (mtp85) cc_final: 0.8567 (mtt-85) REVERT: A 321 ARG cc_start: 0.8727 (ttm-80) cc_final: 0.8361 (ttm-80) REVERT: C 192 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: C 230 MET cc_start: 0.8471 (ttm) cc_final: 0.8250 (ttm) REVERT: E 132 ASP cc_start: 0.8472 (m-30) cc_final: 0.8224 (m-30) REVERT: I 82 MET cc_start: 0.8459 (mtm) cc_final: 0.8249 (mtp) REVERT: L 79 GLN cc_start: 0.7989 (mp10) cc_final: 0.7583 (mp10) REVERT: F 135 ASN cc_start: 0.7856 (p0) cc_final: 0.7404 (p0) outliers start: 80 outliers final: 35 residues processed: 439 average time/residue: 0.7259 time to fit residues: 345.6692 Evaluate side-chains 416 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 380 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 159 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 231 ASN C 94 ASN C 159 ASN E 159 ASN E 165 ASN E 166 GLN I 76 ASN J 31 ASN J 69 ASN J 79 GLN B 30 GLN B 125 GLN B 154 ASN D 43 ASN D 125 GLN F 30 GLN F 43 ASN F 95 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.109365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.101816 restraints weight = 24226.252| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.44 r_work: 0.3370 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17164 Z= 0.224 Angle : 0.562 8.108 23292 Z= 0.300 Chirality : 0.045 0.198 2531 Planarity : 0.004 0.047 3018 Dihedral : 4.960 52.850 2335 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 4.41 % Allowed : 23.81 % Favored : 71.77 % 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: 0.44 (0.18), residues: 2123 helix: 2.49 (0.28), residues: 351 sheet: 0.92 (0.25), residues: 465 loop : -0.58 (0.16), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 123 TYR 0.015 0.001 TYR M 91 PHE 0.015 0.002 PHE F 3 TRP 0.009 0.001 TRP I 47 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00537 (17140) covalent geometry : angle 0.55402 (23244) SS BOND : bond 0.00431 ( 24) SS BOND : angle 2.11441 ( 48) hydrogen bonds : bond 0.04469 ( 672) hydrogen bonds : angle 4.64693 ( 1860) *********************** 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 464 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 383 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 315 ARG cc_start: 0.8774 (mtp85) cc_final: 0.8565 (mtt-85) REVERT: A 321 ARG cc_start: 0.8771 (ttm-80) cc_final: 0.8570 (ttm-80) REVERT: C 92 ASN cc_start: 0.8363 (p0) cc_final: 0.8147 (p0) REVERT: C 192 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: C 230 MET cc_start: 0.8546 (ttm) cc_final: 0.8310 (ttm) REVERT: I 82 MET cc_start: 0.8358 (mtm) cc_final: 0.8062 (mtp) REVERT: D 51 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8195 (tttp) REVERT: F 135 ASN cc_start: 0.8036 (p0) cc_final: 0.7594 (p0) outliers start: 81 outliers final: 46 residues processed: 433 average time/residue: 0.7334 time to fit residues: 344.7745 Evaluate side-chains 425 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 377 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain H residue 2 GLU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 135 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 187 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 282 GLN C 94 ASN C 159 ASN E 159 ASN E 165 ASN I 76 ASN J 31 ASN B 30 GLN B 62 GLN B 125 GLN D 43 ASN F 30 GLN F 43 ASN F 95 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.101470 restraints weight = 24074.776| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.43 r_work: 0.3363 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17164 Z= 0.245 Angle : 0.565 7.873 23292 Z= 0.301 Chirality : 0.046 0.224 2531 Planarity : 0.004 0.048 3018 Dihedral : 4.958 48.981 2333 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.84 % Rotamer: Outliers : 4.90 % Allowed : 23.92 % Favored : 71.17 % 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: 0.45 (0.18), residues: 2123 helix: 2.44 (0.27), residues: 351 sheet: 0.92 (0.25), residues: 470 loop : -0.56 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 123 TYR 0.015 0.002 TYR M 91 PHE 0.015 0.002 PHE C 102 TRP 0.009 0.002 TRP H 47 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00586 (17140) covalent geometry : angle 0.55975 (23244) SS BOND : bond 0.00402 ( 24) SS BOND : angle 1.84694 ( 48) hydrogen bonds : bond 0.04541 ( 672) hydrogen bonds : angle 4.63577 ( 1860) *********************** 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 470 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 380 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 315 ARG cc_start: 0.8778 (mtp85) cc_final: 0.8574 (mtt-85) REVERT: A 321 ARG cc_start: 0.8766 (ttm-80) cc_final: 0.8453 (ttm-80) REVERT: C 92 ASN cc_start: 0.8357 (p0) cc_final: 0.8105 (p0) REVERT: C 192 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: C 230 MET cc_start: 0.8564 (ttm) cc_final: 0.8348 (ttm) REVERT: E 11 ASP cc_start: 0.7176 (t0) cc_final: 0.6915 (t0) REVERT: E 63 LYS cc_start: 0.8545 (ptmm) cc_final: 0.8324 (ptmm) REVERT: I 82 MET cc_start: 0.8436 (mtm) cc_final: 0.8143 (mtp) REVERT: I 100 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7711 (mpm) REVERT: D 51 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8171 (tttp) REVERT: D 135 ASN cc_start: 0.7547 (t0) cc_final: 0.7058 (t0) REVERT: F 135 ASN cc_start: 0.8067 (p0) cc_final: 0.7600 (p0) outliers start: 90 outliers final: 52 residues processed: 437 average time/residue: 0.7028 time to fit residues: 333.4661 Evaluate side-chains 438 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 383 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 222 LYS Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain H residue 2 GLU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 133 optimal weight: 0.9990 chunk 192 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 chunk 184 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 226 GLN C 94 ASN C 159 ASN E 159 ASN E 165 ASN I 76 ASN J 31 ASN J 69 ASN J 79 GLN B 30 GLN B 125 GLN D 43 ASN D 125 GLN F 30 GLN F 43 ASN F 95 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.109408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.101952 restraints weight = 23974.110| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.43 r_work: 0.3372 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17164 Z= 0.193 Angle : 0.553 8.742 23292 Z= 0.295 Chirality : 0.045 0.273 2531 Planarity : 0.004 0.050 3018 Dihedral : 4.816 49.615 2330 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.68 % Favored : 97.22 % Rotamer: Outliers : 4.41 % Allowed : 24.20 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.18), residues: 2123 helix: 2.55 (0.27), residues: 354 sheet: 0.93 (0.26), residues: 440 loop : -0.53 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 321 TYR 0.013 0.001 TYR M 91 PHE 0.012 0.001 PHE A 102 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00461 (17140) covalent geometry : angle 0.54446 (23244) SS BOND : bond 0.00555 ( 24) SS BOND : angle 2.15007 ( 48) hydrogen bonds : bond 0.04339 ( 672) hydrogen bonds : angle 4.56838 ( 1860) *********************** 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 472 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 391 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 321 ARG cc_start: 0.8754 (ttm-80) cc_final: 0.8418 (ttm-80) REVERT: C 92 ASN cc_start: 0.8323 (p0) cc_final: 0.8105 (p0) REVERT: C 192 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: H 111 VAL cc_start: 0.7797 (OUTLIER) cc_final: 0.7443 (p) REVERT: I 82 MET cc_start: 0.8460 (mtm) cc_final: 0.8167 (mtp) REVERT: D 68 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8228 (mmtp) REVERT: F 103 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7288 (mm-30) REVERT: F 135 ASN cc_start: 0.8042 (p0) cc_final: 0.7590 (p0) REVERT: F 151 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8202 (p) outliers start: 81 outliers final: 52 residues processed: 441 average time/residue: 0.7321 time to fit residues: 350.3132 Evaluate side-chains 428 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 372 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 222 LYS Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 92 optimal weight: 0.0870 chunk 26 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 185 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 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 159 ASN A 226 GLN C 159 ASN E 159 ASN E 165 ASN I 76 ASN J 31 ASN B 30 GLN B 125 GLN D 43 ASN F 30 GLN F 43 ASN F 95 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.109635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102184 restraints weight = 23935.060| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.43 r_work: 0.3375 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 17164 Z= 0.181 Angle : 0.559 10.759 23292 Z= 0.298 Chirality : 0.045 0.290 2531 Planarity : 0.004 0.051 3018 Dihedral : 4.735 50.406 2330 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.97 % Favored : 96.94 % Rotamer: Outliers : 5.12 % Allowed : 23.71 % Favored : 71.17 % 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: 0.43 (0.18), residues: 2123 helix: 2.62 (0.27), residues: 354 sheet: 0.77 (0.25), residues: 453 loop : -0.56 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 321 TYR 0.013 0.001 TYR F 24 PHE 0.012 0.001 PHE F 9 TRP 0.009 0.001 TRP M 47 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00435 (17140) covalent geometry : angle 0.54820 (23244) SS BOND : bond 0.00632 ( 24) SS BOND : angle 2.42594 ( 48) hydrogen bonds : bond 0.04280 ( 672) hydrogen bonds : angle 4.53878 ( 1860) *********************** 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 473 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 379 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 295 GLN cc_start: 0.8447 (pp30) cc_final: 0.8055 (pp30) REVERT: A 321 ARG cc_start: 0.8751 (ttm-80) cc_final: 0.8424 (ttm-80) REVERT: C 92 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.8093 (p0) REVERT: E 11 ASP cc_start: 0.7165 (t0) cc_final: 0.6934 (t0) REVERT: H 111 VAL cc_start: 0.7783 (OUTLIER) cc_final: 0.7424 (p) REVERT: F 135 ASN cc_start: 0.8030 (p0) cc_final: 0.7480 (p0) REVERT: F 151 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8246 (p) outliers start: 94 outliers final: 56 residues processed: 435 average time/residue: 0.6891 time to fit residues: 326.4440 Evaluate side-chains 434 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 375 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 222 LYS Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 187 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN C 159 ASN E 159 ASN E 165 ASN I 76 ASN J 31 ASN B 30 GLN B 62 GLN B 125 GLN D 43 ASN F 30 GLN F 43 ASN F 95 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.108484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.101044 restraints weight = 23911.210| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.42 r_work: 0.3358 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 17164 Z= 0.288 Angle : 0.633 12.896 23292 Z= 0.335 Chirality : 0.048 0.330 2531 Planarity : 0.005 0.053 3018 Dihedral : 4.850 48.495 2328 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 4.41 % Allowed : 24.36 % Favored : 71.23 % 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 (0.18), residues: 2123 helix: 2.40 (0.27), residues: 351 sheet: 0.82 (0.26), residues: 431 loop : -0.57 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 321 TYR 0.017 0.002 TYR M 91 PHE 0.019 0.002 PHE A 102 TRP 0.009 0.002 TRP H 47 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00692 (17140) covalent geometry : angle 0.62152 (23244) SS BOND : bond 0.00818 ( 24) SS BOND : angle 2.67901 ( 48) hydrogen bonds : bond 0.04742 ( 672) hydrogen bonds : angle 4.65394 ( 1860) *********************** 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 466 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 385 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7798 (m-40) cc_final: 0.7404 (OUTLIER) REVERT: A 321 ARG cc_start: 0.8785 (ttm-80) cc_final: 0.8464 (ttm-80) REVERT: C 92 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8127 (p0) REVERT: E 11 ASP cc_start: 0.7305 (t0) cc_final: 0.7049 (t0) REVERT: H 111 VAL cc_start: 0.7786 (OUTLIER) cc_final: 0.7429 (p) REVERT: I 82 MET cc_start: 0.8431 (mtm) cc_final: 0.8125 (mtp) REVERT: I 100 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.7650 (mpm) REVERT: F 135 ASN cc_start: 0.8130 (p0) cc_final: 0.7603 (p0) REVERT: F 151 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.8175 (p) outliers start: 81 outliers final: 61 residues processed: 430 average time/residue: 0.7178 time to fit residues: 335.2847 Evaluate side-chains 445 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 381 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 222 LYS Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain H residue 2 GLU Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain M residue 2 GLU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 19 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 189 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 226 GLN C 94 ASN C 159 ASN E 159 ASN E 165 ASN I 76 ASN J 31 ASN B 30 GLN B 62 GLN B 95 ASN B 125 GLN D 43 ASN D 125 GLN F 30 GLN F 43 ASN F 95 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.109442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.101979 restraints weight = 23947.949| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.43 r_work: 0.3371 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17164 Z= 0.184 Angle : 0.583 15.229 23292 Z= 0.310 Chirality : 0.045 0.301 2531 Planarity : 0.004 0.053 3018 Dihedral : 4.729 50.137 2327 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.87 % Favored : 97.03 % Rotamer: Outliers : 4.25 % Allowed : 24.85 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.18), residues: 2123 helix: 2.52 (0.27), residues: 354 sheet: 0.77 (0.26), residues: 431 loop : -0.53 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 321 TYR 0.012 0.001 TYR M 91 PHE 0.012 0.001 PHE F 9 TRP 0.010 0.001 TRP I 47 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00442 (17140) covalent geometry : angle 0.57395 (23244) SS BOND : bond 0.00742 ( 24) SS BOND : angle 2.37924 ( 48) hydrogen bonds : bond 0.04360 ( 672) hydrogen bonds : angle 4.56639 ( 1860) *********************** 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 454 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 376 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 321 ARG cc_start: 0.8770 (ttm-80) cc_final: 0.8458 (ttm-80) REVERT: C 63 LYS cc_start: 0.8586 (ptmm) cc_final: 0.8316 (ptmm) REVERT: C 92 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.8066 (p0) REVERT: E 11 ASP cc_start: 0.7244 (t0) cc_final: 0.6988 (t70) REVERT: H 111 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7414 (p) REVERT: I 82 MET cc_start: 0.8418 (mtm) cc_final: 0.8153 (mtp) REVERT: I 100 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7678 (mpm) REVERT: F 135 ASN cc_start: 0.8110 (p0) cc_final: 0.7574 (p0) REVERT: F 151 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.8185 (p) outliers start: 78 outliers final: 53 residues processed: 424 average time/residue: 0.7222 time to fit residues: 332.9105 Evaluate side-chains 430 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 373 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 222 LYS Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 108 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 27 optimal weight: 0.0030 chunk 60 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN C 94 ASN C 159 ASN E 159 ASN E 165 ASN I 76 ASN J 31 ASN B 30 GLN B 125 GLN D 43 ASN D 125 GLN F 30 GLN F 43 ASN F 95 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.109437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.101969 restraints weight = 23951.602| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.43 r_work: 0.3371 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17164 Z= 0.191 Angle : 0.587 14.218 23292 Z= 0.311 Chirality : 0.045 0.271 2531 Planarity : 0.004 0.053 3018 Dihedral : 4.719 50.255 2327 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.89 % Rotamer: Outliers : 3.60 % Allowed : 25.50 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.18), residues: 2123 helix: 2.54 (0.27), residues: 354 sheet: 0.70 (0.25), residues: 461 loop : -0.55 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 321 TYR 0.013 0.001 TYR M 91 PHE 0.012 0.001 PHE F 9 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00458 (17140) covalent geometry : angle 0.57877 (23244) SS BOND : bond 0.00755 ( 24) SS BOND : angle 2.20298 ( 48) hydrogen bonds : bond 0.04331 ( 672) hydrogen bonds : angle 4.53887 ( 1860) *********************** 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 443 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 377 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 229 ARG cc_start: 0.8895 (mmt-90) cc_final: 0.8552 (mpt180) REVERT: A 321 ARG cc_start: 0.8776 (ttm-80) cc_final: 0.8460 (ttm-80) REVERT: C 44 GLU cc_start: 0.7561 (tp30) cc_final: 0.7188 (tp30) REVERT: C 63 LYS cc_start: 0.8596 (ptmm) cc_final: 0.8357 (pttp) REVERT: C 92 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.8048 (p0) REVERT: E 11 ASP cc_start: 0.7238 (t0) cc_final: 0.6981 (t70) REVERT: H 111 VAL cc_start: 0.7769 (OUTLIER) cc_final: 0.7406 (p) REVERT: I 82 MET cc_start: 0.8391 (mtm) cc_final: 0.8130 (mtp) REVERT: I 100 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7739 (mpm) REVERT: F 135 ASN cc_start: 0.8113 (p0) cc_final: 0.7613 (p0) REVERT: F 151 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8207 (p) outliers start: 66 outliers final: 53 residues processed: 415 average time/residue: 0.7273 time to fit residues: 327.4909 Evaluate side-chains 435 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 378 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 222 LYS Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 202 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN C 94 ASN E 159 ASN E 165 ASN I 76 ASN J 31 ASN B 30 GLN B 125 GLN D 43 ASN D 125 GLN F 30 GLN F 43 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.109566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102116 restraints weight = 23952.559| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.42 r_work: 0.3375 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17164 Z= 0.176 Angle : 0.588 14.068 23292 Z= 0.312 Chirality : 0.045 0.261 2531 Planarity : 0.004 0.053 3018 Dihedral : 4.689 51.013 2327 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 3.38 % Allowed : 26.21 % Favored : 70.41 % 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 (0.18), residues: 2123 helix: 2.57 (0.27), residues: 354 sheet: 0.69 (0.25), residues: 461 loop : -0.54 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 123 TYR 0.012 0.001 TYR M 91 PHE 0.011 0.001 PHE F 9 TRP 0.009 0.001 TRP I 47 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00422 (17140) covalent geometry : angle 0.58108 (23244) SS BOND : bond 0.00704 ( 24) SS BOND : angle 2.11793 ( 48) hydrogen bonds : bond 0.04263 ( 672) hydrogen bonds : angle 4.53074 ( 1860) ********************** 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 453 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 391 time to evaluate : 0.677 Fit side-chains REVERT: A 229 ARG cc_start: 0.8893 (mmt-90) cc_final: 0.8546 (mpt180) REVERT: A 321 ARG cc_start: 0.8775 (ttm-80) cc_final: 0.8454 (ttm-80) REVERT: C 63 LYS cc_start: 0.8593 (ptmm) cc_final: 0.8378 (pttp) REVERT: C 92 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.8032 (p0) REVERT: E 11 ASP cc_start: 0.7235 (t0) cc_final: 0.6980 (t70) REVERT: H 111 VAL cc_start: 0.7771 (OUTLIER) cc_final: 0.7408 (p) REVERT: I 82 MET cc_start: 0.8372 (mtm) cc_final: 0.8117 (mtp) REVERT: F 135 ASN cc_start: 0.8091 (p0) cc_final: 0.7617 (p0) outliers start: 62 outliers final: 52 residues processed: 426 average time/residue: 0.7139 time to fit residues: 330.1693 Evaluate side-chains 435 residues out of total 1838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 381 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 222 LYS Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 0.0870 chunk 74 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 155 optimal weight: 0.2980 chunk 103 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 166 GLN C 159 ASN E 159 ASN E 165 ASN I 76 ASN J 31 ASN B 30 GLN B 125 GLN B 154 ASN D 43 ASN D 125 GLN F 30 GLN F 43 ASN F 95 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102062 restraints weight = 24049.783| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.43 r_work: 0.3375 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17164 Z= 0.188 Angle : 0.619 15.508 23292 Z= 0.325 Chirality : 0.046 0.469 2531 Planarity : 0.004 0.053 3018 Dihedral : 4.602 50.837 2325 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 3.43 % Allowed : 25.89 % Favored : 70.68 % 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: 0.40 (0.18), residues: 2123 helix: 2.52 (0.27), residues: 354 sheet: 0.71 (0.25), residues: 461 loop : -0.55 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 123 TYR 0.015 0.001 TYR F 24 PHE 0.012 0.001 PHE F 9 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00448 (17140) covalent geometry : angle 0.60486 (23244) SS BOND : bond 0.00767 ( 24) SS BOND : angle 2.93596 ( 48) hydrogen bonds : bond 0.04319 ( 672) hydrogen bonds : angle 4.53899 ( 1860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7553.96 seconds wall clock time: 128 minutes 51.91 seconds (7731.91 seconds total)