Starting phenix.real_space_refine on Thu Feb 5 10:24:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mtg_48608/02_2026/9mtg_48608.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mtg_48608/02_2026/9mtg_48608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mtg_48608/02_2026/9mtg_48608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mtg_48608/02_2026/9mtg_48608.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mtg_48608/02_2026/9mtg_48608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mtg_48608/02_2026/9mtg_48608.map" } resolution = 2.52 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 72 5.16 5 C 10383 2.51 5 N 2834 2.21 5 O 3202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 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: 16491 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2526 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 19, 'TRANS': 302} Chain: "C" Number of atoms: 2526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2526 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 19, 'TRANS': 302} Chain: "E" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2518 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 302} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 886 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "I" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 886 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "J" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 750 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 97} Chain: "L" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 758 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "M" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 886 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "N" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 758 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "B" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1335 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain breaks: 1 Chain: "D" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1335 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain breaks: 1 Chain: "F" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1327 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain breaks: 1 Time building chain proxies: 3.64, per 1000 atoms: 0.22 Number of scatterers: 16491 At special positions: 0 Unit cell: (128.018, 120.612, 150.236, 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 72 16.00 O 3202 8.00 N 2834 7.00 C 10383 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.06 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.04 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.01 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.02 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=2.04 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: 1.11 Conformation dependent library (CDL) restraints added in 620.8 milliseconds 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3878 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 45 sheets defined 20.6% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 4.064A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N SER A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) 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 80 removed outlier: 4.029A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N SER C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.498A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 193 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 4.344A pdb=" N GLU E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER E 78 " --> pdb=" O GLU E 75 " (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 83 through 87 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.768A pdb=" N VAL J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.682A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.699A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 60 removed outlier: 4.121A pdb=" N MET B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN B 60 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 127 removed outlier: 3.551A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.752A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 60 removed outlier: 3.963A pdb=" N MET D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN D 60 " --> pdb=" O ILE D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 127 removed outlier: 3.509A pdb=" N GLU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 158 through 170 removed outlier: 3.767A pdb=" N TYR D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLU D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLU D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 74 through 127 removed outlier: 3.580A pdb=" N GLU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 163 through 170 removed outlier: 3.734A pdb=" N ASN F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.377A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.570A pdb=" N ASP A 101 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A 260A" --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 117 " --> pdb=" O GLU A 260A" (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.570A pdb=" N ASP A 101 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.653A 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 281 through 282 Processing sheet with id=AB2, first strand: chain 'D' and resid 31 through 36 removed outlier: 3.901A pdb=" N GLY D 31 " --> pdb=" O ASN D 28 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.429A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) 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: 6.557A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 115 through 121A removed outlier: 6.642A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU C 175 " --> pdb=" O MET C 260 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 115 through 121A removed outlier: 6.642A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU C 175 " --> pdb=" O MET C 260 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.543A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) 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 287 Processing sheet with id=AC3, first strand: chain 'F' and resid 32 through 36 Processing sheet with id=AC4, first strand: chain 'E' and resid 24 through 26 removed outlier: 4.280A pdb=" N ASP E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) 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: 6.489A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.474A pdb=" N ASP E 101 " --> pdb=" O TYR E 232 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU E 175 " --> pdb=" O MET E 260 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU E 260A" --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER E 117 " --> pdb=" O GLU E 260A" (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.474A pdb=" N ASP E 101 " --> pdb=" O TYR E 232 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.730A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (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 281 through 282 Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.532A pdb=" N LYS H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.461A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLY H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 3 through 7 removed outlier: 4.224A pdb=" N LYS I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.409A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.623A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 10 through 11 removed outlier: 4.172A pdb=" N GLY J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.601A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.281A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.281A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 3 through 7 removed outlier: 4.124A pdb=" N LYS M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.692A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL M 34 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.352A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.352A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1878 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: 2.94 Time building geometry restraints manager: 1.59 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: 5391 1.34 - 1.47: 4019 1.47 - 1.59: 7351 1.59 - 1.71: 0 1.71 - 1.84: 96 Bond restraints: 16857 Sorted by residual: bond pdb=" C ASN C 20 " pdb=" N ASN C 21 " ideal model delta sigma weight residual 1.332 1.422 -0.090 1.52e-02 4.33e+03 3.50e+01 bond pdb=" CA SER M 95 " pdb=" CB SER M 95 " ideal model delta sigma weight residual 1.533 1.472 0.061 1.51e-02 4.39e+03 1.64e+01 bond pdb=" CA SER E 116 " pdb=" CB SER E 116 " ideal model delta sigma weight residual 1.537 1.481 0.056 1.38e-02 5.25e+03 1.63e+01 bond pdb=" CA SER E 114 " pdb=" CB SER E 114 " ideal model delta sigma weight residual 1.537 1.480 0.057 1.41e-02 5.03e+03 1.63e+01 bond pdb=" CA SER I 95 " pdb=" CB SER I 95 " ideal model delta sigma weight residual 1.533 1.472 0.061 1.60e-02 3.91e+03 1.46e+01 ... (remaining 16852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 21949 2.06 - 4.12: 763 4.12 - 6.19: 113 6.19 - 8.25: 18 8.25 - 10.31: 7 Bond angle restraints: 22850 Sorted by residual: angle pdb=" C TYR I 90 " pdb=" CA TYR I 90 " pdb=" CB TYR I 90 " ideal model delta sigma weight residual 109.75 120.06 -10.31 1.65e+00 3.67e-01 3.90e+01 angle pdb=" C PHE A 118 " pdb=" CA PHE A 118 " pdb=" CB PHE A 118 " ideal model delta sigma weight residual 110.34 102.36 7.98 1.40e+00 5.10e-01 3.25e+01 angle pdb=" N SER E 116 " pdb=" CA SER E 116 " pdb=" C SER E 116 " ideal model delta sigma weight residual 114.31 106.98 7.33 1.29e+00 6.01e-01 3.22e+01 angle pdb=" C CYS B 137 " pdb=" CA CYS B 137 " pdb=" CB CYS B 137 " ideal model delta sigma weight residual 110.36 100.86 9.50 1.78e+00 3.16e-01 2.85e+01 angle pdb=" C LYS B 127 " pdb=" CA LYS B 127 " pdb=" CB LYS B 127 " ideal model delta sigma weight residual 116.54 110.61 5.93 1.15e+00 7.56e-01 2.66e+01 ... (remaining 22845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 8799 18.03 - 36.07: 934 36.07 - 54.10: 258 54.10 - 72.13: 36 72.13 - 90.17: 24 Dihedral angle restraints: 10051 sinusoidal: 3964 harmonic: 6087 Sorted by residual: dihedral pdb=" CB CYS E 52 " pdb=" SG CYS E 52 " pdb=" SG CYS E 277 " pdb=" CB CYS E 277 " ideal model delta sinusoidal sigma weight residual 93.00 6.24 86.76 1 1.00e+01 1.00e-02 9.06e+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 -2.82 -83.18 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual -86.00 -4.10 -81.90 1 1.00e+01 1.00e-02 8.25e+01 ... (remaining 10048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2108 0.067 - 0.134: 336 0.134 - 0.201: 38 0.201 - 0.269: 6 0.269 - 0.336: 2 Chirality restraints: 2490 Sorted by residual: chirality pdb=" CA LEU H 96 " pdb=" N LEU H 96 " pdb=" C LEU H 96 " pdb=" CB LEU H 96 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA PHE A 118 " pdb=" N PHE A 118 " pdb=" C PHE A 118 " pdb=" CB PHE A 118 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA TYR I 97 " pdb=" N TYR I 97 " pdb=" C TYR I 97 " pdb=" CB TYR I 97 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 2487 not shown) Planarity restraints: 2951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG M 94 " -0.598 9.50e-02 1.11e+02 2.68e-01 4.39e+01 pdb=" NE ARG M 94 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG M 94 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG M 94 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG M 94 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 38 " 0.457 9.50e-02 1.11e+02 2.05e-01 2.57e+01 pdb=" NE ARG H 38 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG H 38 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG H 38 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 38 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 94 " -0.408 9.50e-02 1.11e+02 1.83e-01 2.04e+01 pdb=" NE ARG I 94 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG I 94 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG I 94 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG I 94 " -0.015 2.00e-02 2.50e+03 ... (remaining 2948 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 307 2.66 - 3.22: 14200 3.22 - 3.78: 25618 3.78 - 4.34: 36324 4.34 - 4.90: 60872 Nonbonded interactions: 137321 Sorted by model distance: nonbonded pdb=" OD1 ASN F 128 " pdb=" OH TYR F 159 " model vdw 2.106 3.040 nonbonded pdb=" OH TYR E 17 " pdb=" O ILE F 6 " model vdw 2.108 3.040 nonbonded pdb=" OE2 GLU F 29 " pdb=" NZ LYS F 143 " model vdw 2.124 3.120 nonbonded pdb=" OH TYR C 17 " pdb=" O ILE D 6 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR A 17 " pdb=" O ILE B 6 " model vdw 2.174 3.040 ... (remaining 137316 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 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 76 or (resid 77 and (name N or nam \ e CA or name C or name O or name CB )) or resid 78 through 324)) selection = (chain 'C' and (resid 11 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 76 or (resid 77 and (name N or nam \ e CA or name C or name O or name CB )) or resid 78 through 324)) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 2 through 59 or resid 65 through 170)) selection = (chain 'D' and (resid 2 through 59 or resid 65 through 170)) selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 3 through 105) selection = (chain 'N' and resid 3 through 105) } 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.960 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 : 0.007 0.090 16878 Z= 0.362 Angle : 0.882 10.309 22892 Z= 0.548 Chirality : 0.052 0.336 2490 Planarity : 0.010 0.268 2951 Dihedral : 16.066 90.165 6110 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 1.72 % Allowed : 18.62 % Favored : 79.66 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 1.19 % 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: -0.05 (0.18), residues: 2086 helix: 1.95 (0.28), residues: 364 sheet: 0.76 (0.24), residues: 503 loop : -1.05 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 123 TYR 0.032 0.002 TYR I 91 PHE 0.014 0.002 PHE I 29 TRP 0.012 0.001 TRP D 92 HIS 0.008 0.002 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00670 (16857) covalent geometry : angle 0.87584 (22850) SS BOND : bond 0.01115 ( 21) SS BOND : angle 2.59906 ( 42) hydrogen bonds : bond 0.12674 ( 657) hydrogen bonds : angle 6.06429 ( 1878) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 472 time to evaluate : 0.567 Fit side-chains REVERT: C 21 ASN cc_start: 0.8071 (t0) cc_final: 0.7784 (t160) REVERT: E 106 GLU cc_start: 0.8126 (mp0) cc_final: 0.7769 (mp0) REVERT: E 203 PHE cc_start: 0.8548 (t80) cc_final: 0.8319 (t80) REVERT: I 94 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8445 (ppt170) REVERT: D 28 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7393 (m-40) REVERT: D 68 LYS cc_start: 0.8739 (mttm) cc_final: 0.8523 (mttp) REVERT: D 170 ARG cc_start: 0.8769 (ttm110) cc_final: 0.8556 (ttm170) outliers start: 31 outliers final: 17 residues processed: 490 average time/residue: 0.6685 time to fit residues: 357.6188 Evaluate side-chains 479 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 460 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 118 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 165 ASN A 226 GLN E 33 ASN E 165 ASN E 226 GLN H 76 ASN I 76 ASN J 92 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN N 92 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 169 ASN D 30 GLN D 169 ASN F 27 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.111409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.103624 restraints weight = 22442.941| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.49 r_work: 0.3300 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16878 Z= 0.140 Angle : 0.559 6.109 22892 Z= 0.297 Chirality : 0.043 0.200 2490 Planarity : 0.004 0.057 2951 Dihedral : 5.756 59.046 2324 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 3.72 % Allowed : 17.79 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.18), residues: 2086 helix: 2.46 (0.28), residues: 361 sheet: 1.00 (0.25), residues: 458 loop : -1.06 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 123 TYR 0.018 0.002 TYR A 201 PHE 0.011 0.001 PHE B 9 TRP 0.009 0.001 TRP D 92 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00331 (16857) covalent geometry : angle 0.55277 (22850) SS BOND : bond 0.00536 ( 21) SS BOND : angle 2.03355 ( 42) hydrogen bonds : bond 0.04469 ( 657) hydrogen bonds : angle 4.68552 ( 1878) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 457 time to evaluate : 0.641 Fit side-chains REVERT: A 109 ARG cc_start: 0.8662 (mtp85) cc_final: 0.8447 (mtm180) REVERT: A 224 ARG cc_start: 0.8474 (mtt-85) cc_final: 0.8225 (mtt-85) REVERT: C 21 ASN cc_start: 0.8387 (t0) cc_final: 0.8011 (t160) REVERT: C 106 GLU cc_start: 0.8169 (mp0) cc_final: 0.7885 (mp0) REVERT: E 21 ASN cc_start: 0.7994 (t0) cc_final: 0.7765 (t160) REVERT: E 203 PHE cc_start: 0.8501 (t80) cc_final: 0.8263 (t80) REVERT: I 86 ASP cc_start: 0.8363 (m-30) cc_final: 0.8015 (m-30) REVERT: L 90 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: N 22 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8422 (m) REVERT: B 150 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6527 (tm-30) REVERT: D 123 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7704 (ttp80) REVERT: D 124 ASN cc_start: 0.8417 (m110) cc_final: 0.8061 (m-40) REVERT: D 165 GLU cc_start: 0.7311 (mp0) cc_final: 0.7025 (mp0) REVERT: F 58 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8177 (tppt) outliers start: 67 outliers final: 33 residues processed: 494 average time/residue: 0.6513 time to fit residues: 352.0542 Evaluate side-chains 482 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 446 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 58 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 165 ASN A 226 GLN C 33 ASN C 231 ASN E 33 ASN E 165 ASN E 191 GLN E 226 GLN I 76 ASN J 92 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 169 ASN D 135 ASN D 169 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.109912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.102025 restraints weight = 22827.365| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.52 r_work: 0.3271 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16878 Z= 0.220 Angle : 0.591 7.125 22892 Z= 0.312 Chirality : 0.045 0.252 2490 Planarity : 0.004 0.054 2951 Dihedral : 5.321 59.595 2302 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 4.45 % Allowed : 18.01 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.18), residues: 2086 helix: 2.48 (0.27), residues: 361 sheet: 0.98 (0.24), residues: 461 loop : -1.06 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 123 TYR 0.021 0.002 TYR A 201 PHE 0.013 0.002 PHE B 9 TRP 0.012 0.001 TRP D 92 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00534 (16857) covalent geometry : angle 0.58505 (22850) SS BOND : bond 0.00492 ( 21) SS BOND : angle 1.96593 ( 42) hydrogen bonds : bond 0.04741 ( 657) hydrogen bonds : angle 4.62369 ( 1878) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 464 time to evaluate : 0.573 Fit side-chains REVERT: A 224 ARG cc_start: 0.8501 (mtt-85) cc_final: 0.8203 (mtt-85) REVERT: C 94 ASN cc_start: 0.7797 (m-40) cc_final: 0.7449 (m110) REVERT: C 133 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8391 (mtpp) REVERT: E 21 ASN cc_start: 0.8101 (t0) cc_final: 0.7821 (t160) REVERT: E 203 PHE cc_start: 0.8510 (t80) cc_final: 0.8270 (t80) REVERT: I 39 GLN cc_start: 0.8653 (tt0) cc_final: 0.8453 (tt0) REVERT: I 82 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8454 (mtp) REVERT: L 90 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: M 82 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8496 (mtp) REVERT: N 3 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7892 (mm-40) REVERT: B 57 GLU cc_start: 0.7835 (tp30) cc_final: 0.7606 (tp30) REVERT: B 150 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6811 (tm-30) REVERT: D 22 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: D 68 LYS cc_start: 0.8690 (mttm) cc_final: 0.8447 (mttp) REVERT: D 124 ASN cc_start: 0.8461 (m110) cc_final: 0.8102 (m-40) REVERT: D 150 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6852 (tm-30) REVERT: D 165 GLU cc_start: 0.7328 (mp0) cc_final: 0.6933 (mp0) REVERT: F 30 GLN cc_start: 0.8552 (mt0) cc_final: 0.8351 (mt0) outliers start: 80 outliers final: 52 residues processed: 501 average time/residue: 0.6172 time to fit residues: 339.3134 Evaluate side-chains 517 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 460 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 304 LYS Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 188 optimal weight: 0.1980 chunk 204 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 165 ASN A 226 GLN C 33 ASN E 33 ASN E 165 ASN E 226 GLN I 76 ASN J 92 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN B 28 ASN B 125 GLN B 169 ASN D 30 GLN D 169 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.110709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.102876 restraints weight = 22643.306| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.50 r_work: 0.3288 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16878 Z= 0.157 Angle : 0.550 8.415 22892 Z= 0.290 Chirality : 0.043 0.255 2490 Planarity : 0.004 0.053 2951 Dihedral : 5.101 59.769 2300 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.12 % Rotamer: Outliers : 4.28 % Allowed : 18.73 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.18), residues: 2086 helix: 2.67 (0.27), residues: 361 sheet: 0.89 (0.24), residues: 488 loop : -0.97 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 123 TYR 0.023 0.002 TYR A 201 PHE 0.011 0.001 PHE B 9 TRP 0.010 0.001 TRP D 92 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00377 (16857) covalent geometry : angle 0.54434 (22850) SS BOND : bond 0.00481 ( 21) SS BOND : angle 1.86044 ( 42) hydrogen bonds : bond 0.04368 ( 657) hydrogen bonds : angle 4.47191 ( 1878) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 469 time to evaluate : 0.548 Fit side-chains REVERT: A 109 ARG cc_start: 0.8679 (mtp85) cc_final: 0.8420 (mtm180) REVERT: A 224 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.8202 (mtt-85) REVERT: A 295 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8210 (pt0) REVERT: C 94 ASN cc_start: 0.7782 (m-40) cc_final: 0.7443 (m110) REVERT: C 174 LYS cc_start: 0.8662 (mttp) cc_final: 0.8439 (mtmt) REVERT: C 313 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8302 (tptp) REVERT: C 320 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8063 (mt) REVERT: E 21 ASN cc_start: 0.8073 (t0) cc_final: 0.7812 (t160) REVERT: E 203 PHE cc_start: 0.8600 (t80) cc_final: 0.8396 (t80) REVERT: H 82 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8234 (mtp) REVERT: I 82 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8411 (mtp) REVERT: L 90 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: M 82 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8442 (mtp) REVERT: N 22 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8418 (m) REVERT: B 57 GLU cc_start: 0.7806 (tp30) cc_final: 0.7590 (tp30) REVERT: B 150 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6785 (tm-30) REVERT: D 68 LYS cc_start: 0.8682 (mttm) cc_final: 0.8443 (mttp) REVERT: D 124 ASN cc_start: 0.8408 (m110) cc_final: 0.8177 (m-40) REVERT: D 161 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7808 (tttm) REVERT: D 165 GLU cc_start: 0.7335 (mp0) cc_final: 0.6930 (mp0) REVERT: F 30 GLN cc_start: 0.8484 (mt0) cc_final: 0.8214 (mt0) REVERT: F 58 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8173 (tppt) outliers start: 77 outliers final: 43 residues processed: 503 average time/residue: 0.6611 time to fit residues: 364.1304 Evaluate side-chains 503 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 450 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 105 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 19 optimal weight: 0.6980 chunk 77 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 165 ASN A 226 GLN C 33 ASN E 33 ASN E 165 ASN E 191 GLN E 226 GLN I 39 GLN I 76 ASN J 92 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 169 ASN D 135 ASN D 169 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.109686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.101807 restraints weight = 22589.819| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.50 r_work: 0.3271 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 16878 Z= 0.224 Angle : 0.590 11.374 22892 Z= 0.311 Chirality : 0.045 0.296 2490 Planarity : 0.004 0.055 2951 Dihedral : 5.237 58.941 2300 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 5.06 % Allowed : 18.51 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2086 helix: 2.60 (0.27), residues: 361 sheet: 0.85 (0.23), residues: 488 loop : -1.00 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 123 TYR 0.024 0.002 TYR A 201 PHE 0.012 0.002 PHE F 9 TRP 0.013 0.001 TRP D 92 HIS 0.005 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00540 (16857) covalent geometry : angle 0.58507 (22850) SS BOND : bond 0.00550 ( 21) SS BOND : angle 1.89433 ( 42) hydrogen bonds : bond 0.04687 ( 657) hydrogen bonds : angle 4.53795 ( 1878) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 446 time to evaluate : 0.553 Fit side-chains REVERT: A 44 GLU cc_start: 0.7743 (tp30) cc_final: 0.7510 (tp30) REVERT: A 224 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.8182 (mtt-85) REVERT: A 295 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8224 (pt0) REVERT: C 225 ASP cc_start: 0.7619 (t70) cc_final: 0.7413 (t70) REVERT: C 313 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8268 (tptp) REVERT: C 320 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8089 (mt) REVERT: E 21 ASN cc_start: 0.8132 (t0) cc_final: 0.7784 (t160) REVERT: E 203 PHE cc_start: 0.8608 (t80) cc_final: 0.8405 (t80) REVERT: H 82 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8254 (mtp) REVERT: L 90 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: M 82 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8484 (mtp) REVERT: B 29 GLU cc_start: 0.7447 (pm20) cc_final: 0.7122 (pm20) REVERT: B 57 GLU cc_start: 0.7834 (tp30) cc_final: 0.7620 (tp30) REVERT: B 150 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6838 (tm-30) REVERT: D 22 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: D 68 LYS cc_start: 0.8673 (mttm) cc_final: 0.8445 (mttp) REVERT: D 161 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7811 (tttm) REVERT: D 165 GLU cc_start: 0.7393 (mp0) cc_final: 0.6994 (mp0) REVERT: F 30 GLN cc_start: 0.8526 (mt0) cc_final: 0.8205 (mt0) REVERT: F 57 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6911 (mm-30) outliers start: 91 outliers final: 59 residues processed: 485 average time/residue: 0.6313 time to fit residues: 334.8011 Evaluate side-chains 525 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 458 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 164 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 178 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 151 optimal weight: 0.0970 chunk 155 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 226 GLN C 33 ASN E 33 ASN E 165 ASN E 226 GLN I 39 GLN I 76 ASN J 92 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 125 GLN B 169 ASN D 169 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.110972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.103280 restraints weight = 22470.763| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.45 r_work: 0.3302 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16878 Z= 0.161 Angle : 0.548 11.479 22892 Z= 0.291 Chirality : 0.043 0.283 2490 Planarity : 0.004 0.054 2951 Dihedral : 5.099 58.729 2300 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.68 % Favored : 97.27 % Rotamer: Outliers : 4.28 % Allowed : 19.90 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 2086 helix: 2.71 (0.27), residues: 361 sheet: 0.89 (0.24), residues: 488 loop : -0.97 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 123 TYR 0.023 0.002 TYR A 201 PHE 0.011 0.001 PHE B 9 TRP 0.010 0.001 TRP D 92 HIS 0.003 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00388 (16857) covalent geometry : angle 0.54294 (22850) SS BOND : bond 0.00500 ( 21) SS BOND : angle 1.77518 ( 42) hydrogen bonds : bond 0.04366 ( 657) hydrogen bonds : angle 4.43144 ( 1878) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 465 time to evaluate : 0.618 Fit side-chains REVERT: A 44 GLU cc_start: 0.7695 (tp30) cc_final: 0.7459 (tp30) REVERT: A 109 ARG cc_start: 0.8679 (mtp85) cc_final: 0.8406 (mtm180) REVERT: A 224 ARG cc_start: 0.8476 (mtt-85) cc_final: 0.8248 (mtt-85) REVERT: A 295 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8190 (pt0) REVERT: C 133 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8380 (mtpp) REVERT: C 313 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8231 (tptp) REVERT: C 320 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8081 (mt) REVERT: E 21 ASN cc_start: 0.8088 (t0) cc_final: 0.7752 (t160) REVERT: E 106 GLU cc_start: 0.7984 (mp0) cc_final: 0.7671 (mp0) REVERT: E 203 PHE cc_start: 0.8599 (t80) cc_final: 0.8329 (t80) REVERT: H 82 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8212 (mtp) REVERT: L 90 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: M 82 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8446 (mtp) REVERT: N 22 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8384 (m) REVERT: B 29 GLU cc_start: 0.7322 (pm20) cc_final: 0.7002 (pm20) REVERT: B 150 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6802 (tm-30) REVERT: D 22 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: D 150 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6853 (tm-30) REVERT: D 161 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7775 (tttm) REVERT: D 165 GLU cc_start: 0.7366 (mp0) cc_final: 0.7049 (mp0) REVERT: F 30 GLN cc_start: 0.8520 (mt0) cc_final: 0.8216 (mt0) REVERT: F 57 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6913 (mm-30) REVERT: F 58 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8174 (tppt) REVERT: F 69 GLU cc_start: 0.7539 (mp0) cc_final: 0.7250 (mt-10) outliers start: 77 outliers final: 47 residues processed: 499 average time/residue: 0.6460 time to fit residues: 352.7190 Evaluate side-chains 521 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 464 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 164 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 122 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 131 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 226 GLN C 33 ASN E 33 ASN E 165 ASN E 191 GLN E 226 GLN I 39 GLN I 76 ASN J 92 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 169 ASN D 124 ASN D 135 ASN D 169 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.110003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.102131 restraints weight = 22573.650| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.50 r_work: 0.3289 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16878 Z= 0.201 Angle : 0.573 10.130 22892 Z= 0.303 Chirality : 0.044 0.266 2490 Planarity : 0.004 0.054 2951 Dihedral : 5.175 57.986 2300 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.74 % Rotamer: Outliers : 4.67 % Allowed : 19.84 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.21 (0.18), residues: 2086 helix: 2.66 (0.27), residues: 361 sheet: 0.85 (0.23), residues: 488 loop : -0.98 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 123 TYR 0.024 0.002 TYR A 201 PHE 0.012 0.002 PHE F 9 TRP 0.012 0.001 TRP D 92 HIS 0.004 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00486 (16857) covalent geometry : angle 0.56793 (22850) SS BOND : bond 0.00501 ( 21) SS BOND : angle 1.82018 ( 42) hydrogen bonds : bond 0.04551 ( 657) hydrogen bonds : angle 4.48954 ( 1878) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 466 time to evaluate : 0.545 Fit side-chains REVERT: A 44 GLU cc_start: 0.7740 (tp30) cc_final: 0.7481 (tp30) REVERT: A 224 ARG cc_start: 0.8489 (mtt-85) cc_final: 0.8212 (mtt-85) REVERT: A 295 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8224 (pt0) REVERT: C 133 LYS cc_start: 0.8693 (mtmt) cc_final: 0.8398 (mtpp) REVERT: C 313 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8300 (tptp) REVERT: C 320 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8095 (mt) REVERT: E 21 ASN cc_start: 0.8151 (t0) cc_final: 0.7767 (t160) REVERT: E 203 PHE cc_start: 0.8609 (t80) cc_final: 0.8404 (t80) REVERT: H 82 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8222 (mtp) REVERT: H 82 LEU cc_start: 0.8671 (mt) cc_final: 0.8434 (mt) REVERT: I 82 MET cc_start: 0.8616 (mtm) cc_final: 0.8395 (mtp) REVERT: L 90 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: M 82 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8464 (mtp) REVERT: N 30 SER cc_start: 0.7955 (t) cc_final: 0.7751 (p) REVERT: B 29 GLU cc_start: 0.7346 (pm20) cc_final: 0.6980 (pm20) REVERT: B 150 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6846 (tm-30) REVERT: D 22 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: D 150 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6859 (tm-30) REVERT: D 161 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7822 (tttm) REVERT: D 165 GLU cc_start: 0.7370 (mp0) cc_final: 0.6987 (mp0) REVERT: F 30 GLN cc_start: 0.8533 (mt0) cc_final: 0.8192 (mt0) REVERT: F 57 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6998 (mm-30) REVERT: F 69 GLU cc_start: 0.7524 (mp0) cc_final: 0.7234 (mt-10) outliers start: 84 outliers final: 61 residues processed: 500 average time/residue: 0.6517 time to fit residues: 355.7707 Evaluate side-chains 530 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 461 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 164 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 200 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 45 optimal weight: 0.0980 chunk 108 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 226 GLN C 165 ASN E 33 ASN E 165 ASN E 226 GLN I 39 GLN I 76 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 125 GLN B 169 ASN D 124 ASN D 135 ASN D 169 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.111445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.103775 restraints weight = 22565.025| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.46 r_work: 0.3298 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16878 Z= 0.134 Angle : 0.544 11.154 22892 Z= 0.287 Chirality : 0.043 0.266 2490 Planarity : 0.004 0.054 2951 Dihedral : 4.992 57.969 2300 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.36 % Rotamer: Outliers : 3.84 % Allowed : 20.90 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.18), residues: 2086 helix: 2.79 (0.27), residues: 361 sheet: 0.89 (0.24), residues: 488 loop : -0.90 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 123 TYR 0.023 0.001 TYR A 201 PHE 0.010 0.001 PHE F 138 TRP 0.009 0.001 TRP D 92 HIS 0.003 0.001 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00321 (16857) covalent geometry : angle 0.53794 (22850) SS BOND : bond 0.00567 ( 21) SS BOND : angle 1.90326 ( 42) hydrogen bonds : bond 0.04183 ( 657) hydrogen bonds : angle 4.36063 ( 1878) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 462 time to evaluate : 0.589 Fit side-chains REVERT: A 109 ARG cc_start: 0.8672 (mtp85) cc_final: 0.8452 (mtm180) REVERT: A 224 ARG cc_start: 0.8433 (mtt-85) cc_final: 0.8223 (mtt-85) REVERT: C 94 ASN cc_start: 0.7702 (m-40) cc_final: 0.7416 (m110) REVERT: C 133 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8406 (mtpp) REVERT: C 225 ASP cc_start: 0.7609 (t70) cc_final: 0.7397 (t70) REVERT: C 313 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8247 (tptp) REVERT: E 21 ASN cc_start: 0.8084 (t0) cc_final: 0.7725 (t160) REVERT: E 203 PHE cc_start: 0.8583 (t80) cc_final: 0.8317 (t80) REVERT: H 82 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8208 (mtp) REVERT: H 82 LEU cc_start: 0.8670 (mt) cc_final: 0.8459 (mt) REVERT: L 90 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: M 82 MET cc_start: 0.8694 (mtm) cc_final: 0.8439 (mtp) REVERT: N 22 THR cc_start: 0.8660 (p) cc_final: 0.8422 (m) REVERT: B 29 GLU cc_start: 0.7290 (pm20) cc_final: 0.6979 (pm20) REVERT: B 150 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6813 (tm-30) REVERT: D 22 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: D 165 GLU cc_start: 0.7349 (mp0) cc_final: 0.7103 (mp0) REVERT: F 30 GLN cc_start: 0.8536 (mt0) cc_final: 0.8213 (mt0) REVERT: F 57 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7031 (mm-30) REVERT: F 69 GLU cc_start: 0.7524 (mp0) cc_final: 0.7303 (mp0) outliers start: 69 outliers final: 41 residues processed: 493 average time/residue: 0.6471 time to fit residues: 349.0891 Evaluate side-chains 494 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 449 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 164 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 170 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 147 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 226 GLN C 231 ASN E 33 ASN E 165 ASN E 191 GLN E 226 GLN I 76 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN B 125 GLN B 169 ASN D 124 ASN D 135 ASN D 169 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.103188 restraints weight = 22586.235| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.50 r_work: 0.3304 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16878 Z= 0.145 Angle : 0.557 12.856 22892 Z= 0.293 Chirality : 0.043 0.283 2490 Planarity : 0.004 0.053 2951 Dihedral : 4.973 57.560 2300 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 3.00 % Allowed : 21.96 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.34 (0.18), residues: 2086 helix: 2.80 (0.27), residues: 361 sheet: 0.87 (0.23), residues: 488 loop : -0.88 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 123 TYR 0.022 0.001 TYR H 97 PHE 0.011 0.001 PHE B 9 TRP 0.010 0.001 TRP D 92 HIS 0.003 0.001 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00350 (16857) covalent geometry : angle 0.55188 (22850) SS BOND : bond 0.00610 ( 21) SS BOND : angle 1.88080 ( 42) hydrogen bonds : bond 0.04193 ( 657) hydrogen bonds : angle 4.36648 ( 1878) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 453 time to evaluate : 0.549 Fit side-chains REVERT: A 109 ARG cc_start: 0.8675 (mtp85) cc_final: 0.8414 (mtm180) REVERT: A 224 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.8216 (mtt-85) REVERT: C 94 ASN cc_start: 0.7779 (m-40) cc_final: 0.7391 (m110) REVERT: C 133 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8376 (mtpp) REVERT: C 199 ASP cc_start: 0.7641 (p0) cc_final: 0.7396 (p0) REVERT: C 225 ASP cc_start: 0.7627 (t70) cc_final: 0.7400 (t70) REVERT: C 313 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8284 (tptp) REVERT: E 21 ASN cc_start: 0.8136 (t0) cc_final: 0.7723 (t160) REVERT: E 203 PHE cc_start: 0.8583 (t80) cc_final: 0.8304 (t80) REVERT: H 82 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8217 (mtp) REVERT: H 82 LEU cc_start: 0.8651 (mt) cc_final: 0.8444 (mt) REVERT: M 82 MET cc_start: 0.8711 (mtm) cc_final: 0.8449 (mtp) REVERT: N 22 THR cc_start: 0.8687 (p) cc_final: 0.8449 (m) REVERT: B 28 ASN cc_start: 0.7574 (m-40) cc_final: 0.7319 (m110) REVERT: B 29 GLU cc_start: 0.7338 (pm20) cc_final: 0.7004 (pm20) REVERT: B 149 MET cc_start: 0.8278 (mtt) cc_final: 0.7731 (mtt) REVERT: B 150 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6869 (tm-30) REVERT: D 22 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.7878 (m-80) REVERT: D 165 GLU cc_start: 0.7347 (mp0) cc_final: 0.7052 (mp0) REVERT: F 30 GLN cc_start: 0.8494 (mt0) cc_final: 0.8170 (mt0) outliers start: 54 outliers final: 46 residues processed: 475 average time/residue: 0.6332 time to fit residues: 329.8251 Evaluate side-chains 490 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 441 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 164 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 167 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 108 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 0.0370 chunk 205 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 142 optimal weight: 0.0980 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 226 GLN E 33 ASN E 165 ASN E 226 GLN I 39 GLN I 76 ASN L 90 GLN N 92 ASN B 125 GLN B 169 ASN D 135 ASN D 169 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.112022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.104158 restraints weight = 22547.483| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.50 r_work: 0.3308 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16878 Z= 0.117 Angle : 0.539 10.979 22892 Z= 0.283 Chirality : 0.042 0.238 2490 Planarity : 0.004 0.053 2951 Dihedral : 4.843 57.298 2300 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.36 % Rotamer: Outliers : 2.83 % Allowed : 22.68 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 2086 helix: 2.92 (0.27), residues: 361 sheet: 0.94 (0.23), residues: 488 loop : -0.82 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 123 TYR 0.024 0.001 TYR A 201 PHE 0.009 0.001 PHE B 9 TRP 0.008 0.001 TRP D 92 HIS 0.005 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00278 (16857) covalent geometry : angle 0.53425 (22850) SS BOND : bond 0.00555 ( 21) SS BOND : angle 1.69851 ( 42) hydrogen bonds : bond 0.03963 ( 657) hydrogen bonds : angle 4.26821 ( 1878) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 446 time to evaluate : 0.434 Fit side-chains REVERT: A 109 ARG cc_start: 0.8652 (mtp85) cc_final: 0.8424 (mtm180) REVERT: C 21 ASN cc_start: 0.8356 (t0) cc_final: 0.8133 (t0) REVERT: C 94 ASN cc_start: 0.7749 (m-40) cc_final: 0.7422 (m110) REVERT: C 313 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8263 (tptp) REVERT: E 21 ASN cc_start: 0.8115 (t0) cc_final: 0.7708 (t160) REVERT: E 203 PHE cc_start: 0.8581 (t80) cc_final: 0.8298 (t80) REVERT: H 82 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8160 (mtp) REVERT: M 82 MET cc_start: 0.8705 (mtm) cc_final: 0.8432 (mtp) REVERT: B 29 GLU cc_start: 0.7323 (pm20) cc_final: 0.7028 (pm20) REVERT: B 149 MET cc_start: 0.8159 (mtt) cc_final: 0.7540 (mtt) REVERT: B 150 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6918 (tm-30) REVERT: D 22 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: D 165 GLU cc_start: 0.7318 (mp0) cc_final: 0.7045 (mp0) REVERT: F 30 GLN cc_start: 0.8505 (mt0) cc_final: 0.8175 (mt0) outliers start: 51 outliers final: 39 residues processed: 473 average time/residue: 0.6588 time to fit residues: 341.0606 Evaluate side-chains 488 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 446 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 164 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 192 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 134 optimal weight: 0.0270 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 164 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 190 optimal weight: 0.0970 chunk 127 optimal weight: 0.5980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 165 ASN A 226 GLN E 33 ASN E 165 ASN E 191 GLN E 226 GLN I 39 GLN I 76 ASN L 90 GLN B 125 GLN B 169 ASN D 135 ASN D 169 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.111922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104061 restraints weight = 22630.325| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.50 r_work: 0.3305 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16878 Z= 0.143 Angle : 0.755 59.200 22892 Z= 0.428 Chirality : 0.044 0.616 2490 Planarity : 0.004 0.053 2951 Dihedral : 4.861 57.266 2300 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.36 % Rotamer: Outliers : 2.78 % Allowed : 23.18 % Favored : 74.04 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.19 % 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: 2086 helix: 2.92 (0.27), residues: 361 sheet: 0.93 (0.23), residues: 488 loop : -0.81 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 109 TYR 0.022 0.001 TYR A 201 PHE 0.009 0.001 PHE F 9 TRP 0.008 0.001 TRP D 92 HIS 0.006 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00323 (16857) covalent geometry : angle 0.75201 (22850) SS BOND : bond 0.00549 ( 21) SS BOND : angle 1.67119 ( 42) hydrogen bonds : bond 0.04013 ( 657) hydrogen bonds : angle 4.26713 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7015.71 seconds wall clock time: 119 minutes 50.59 seconds (7190.59 seconds total)