Starting phenix.real_space_refine on Thu Mar 5 00:09:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o8r_70234/03_2026/9o8r_70234.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o8r_70234/03_2026/9o8r_70234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o8r_70234/03_2026/9o8r_70234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o8r_70234/03_2026/9o8r_70234.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o8r_70234/03_2026/9o8r_70234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o8r_70234/03_2026/9o8r_70234.map" } resolution = 2.96 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= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 10743 2.51 5 N 2919 2.21 5 O 3369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17109 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2528 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain: "B" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1355 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain: "H" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 951 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 771 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "C" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2528 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain: "E" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1355 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain: "G" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 951 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 771 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2528 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain: "F" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1355 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain: "I" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 951 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 771 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.13, per 1000 atoms: 0.24 Number of scatterers: 17109 At special positions: 0 Unit cell: (124.7, 129.775, 143.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3369 8.00 N 2919 7.00 C 10743 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 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 B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS E 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.02 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 144 " - pdb=" SG CYS E 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 277 " distance=2.04 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 76 " distance=2.02 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 33 " " NAG A 403 " - " ASN A 278 " " NAG A 404 " - " ASN A 289 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 21 " " NAG C 402 " - " ASN C 33 " " NAG C 403 " - " ASN C 278 " " NAG C 404 " - " ASN C 289 " " NAG D 401 " - " ASN D 21 " " NAG D 402 " - " ASN D 33 " " NAG D 403 " - " ASN D 278 " " NAG D 404 " - " ASN D 289 " " NAG E 301 " - " ASN E 154 " " NAG F 301 " - " ASN F 154 " " NAG M 1 " - " ASN A 94 " " NAG N 1 " - " ASN C 94 " " NAG O 1 " - " ASN D 94 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3918 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 51 sheets defined 20.3% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.503A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 125 through 127 removed outlier: 4.486A pdb=" N TRP A 127 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 126 Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 171 removed outlier: 4.143A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.625A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.506A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 125 through 127 removed outlier: 4.485A pdb=" N TRP C 127 " --> pdb=" O LYS C 125A" (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'E' and resid 37 through 58 Processing helix chain 'E' and resid 74 through 126 Processing helix chain 'E' and resid 145 through 154 Processing helix chain 'E' and resid 158 through 171 removed outlier: 4.153A pdb=" N TYR E 162 " --> pdb=" O ASP E 158 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU E 165 " --> pdb=" O LYS E 161 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.621A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.504A pdb=" N GLU D 77 " --> pdb=" O PRO D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 125 through 127 removed outlier: 4.482A pdb=" N TRP D 127 " --> pdb=" O LYS D 125A" (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 74 through 126 Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 158 through 171 removed outlier: 4.160A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.621A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.673A pdb=" N GLY B 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) 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 51 through 54 removed outlier: 5.537A pdb=" N LEU A 51 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.557A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 119 through 121 removed outlier: 8.024A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 119 through 121 Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.776A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.533A pdb=" N TYR A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 281 through 282 removed outlier: 3.500A pdb=" N GLY A 303 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR B 64 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.732A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.184A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.011A pdb=" N PHE H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AB7, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AB8, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.510A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS L 38 " --> pdb=" O ASP L 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 31 through 36 removed outlier: 3.669A pdb=" N GLY E 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC2, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.541A pdb=" N LEU C 51 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.558A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 119 through 121 removed outlier: 8.026A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AC8, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.769A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.530A pdb=" N TYR C 209 " --> pdb=" O THR C 206 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 281 through 282 removed outlier: 3.641A pdb=" N THR E 64 " --> pdb=" O GLY C 303 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.734A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.184A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.008A pdb=" N PHE G 102 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 9 through 13 Processing sheet with id=AD6, first strand: chain 'J' and resid 18 through 24 Processing sheet with id=AD7, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.510A pdb=" N TRP J 35 " --> pdb=" O MET J 47 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS J 38 " --> pdb=" O ASP J 85 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 31 through 36 removed outlier: 3.660A pdb=" N GLY F 23 " --> pdb=" O GLY D 16 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 25 through 26 Processing sheet with id=AE1, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AE2, first strand: chain 'D' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'D' and resid 51 through 54 removed outlier: 5.540A pdb=" N LEU D 51 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N CYS D 277 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.557A pdb=" N LEU D 59 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE D 87 " --> pdb=" O ILE D 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 119 through 121 removed outlier: 8.020A pdb=" N LEU D 179 " --> pdb=" O PRO D 254 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 119 through 121 Processing sheet with id=AE7, first strand: chain 'D' and resid 136 through 141 removed outlier: 4.769A pdb=" N CYS D 139 " --> pdb=" O SER D 146 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 164 through 169 removed outlier: 3.531A pdb=" N TYR D 209 " --> pdb=" O THR D 206 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 281 through 282 removed outlier: 3.643A pdb=" N THR F 64 " --> pdb=" O GLY D 303 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.735A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.177A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.006A pdb=" N PHE I 102 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 9 through 13 Processing sheet with id=AF5, first strand: chain 'K' and resid 18 through 24 Processing sheet with id=AF6, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.510A pdb=" N TRP K 35 " --> pdb=" O MET K 47 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS K 38 " --> pdb=" O ASP K 85 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 2.36 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: 5519 1.34 - 1.46: 3523 1.46 - 1.58: 8358 1.58 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 17505 Sorted by residual: bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N GLN G 1 " pdb=" CA GLN G 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" N GLN I 1 " pdb=" CA GLN I 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 bond pdb=" C1 NAG C 404 " pdb=" O5 NAG C 404 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 NAG D 404 " pdb=" O5 NAG D 404 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.02e+00 ... (remaining 17500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 22091 1.21 - 2.42: 1362 2.42 - 3.63: 159 3.63 - 4.84: 85 4.84 - 6.05: 24 Bond angle restraints: 23721 Sorted by residual: angle pdb=" CA MET J 47 " pdb=" CB MET J 47 " pdb=" CG MET J 47 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.16e+00 angle pdb=" CA MET K 47 " pdb=" CB MET K 47 " pdb=" CG MET K 47 " ideal model delta sigma weight residual 114.10 120.13 -6.03 2.00e+00 2.50e-01 9.09e+00 angle pdb=" CA MET L 47 " pdb=" CB MET L 47 " pdb=" CG MET L 47 " ideal model delta sigma weight residual 114.10 120.05 -5.95 2.00e+00 2.50e-01 8.86e+00 angle pdb=" CA GLN J 79 " pdb=" CB GLN J 79 " pdb=" CG GLN J 79 " ideal model delta sigma weight residual 114.10 119.26 -5.16 2.00e+00 2.50e-01 6.67e+00 angle pdb=" CA GLN K 79 " pdb=" CB GLN K 79 " pdb=" CG GLN K 79 " ideal model delta sigma weight residual 114.10 119.23 -5.13 2.00e+00 2.50e-01 6.58e+00 ... (remaining 23716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 9995 16.84 - 33.67: 438 33.67 - 50.51: 148 50.51 - 67.34: 27 67.34 - 84.18: 15 Dihedral angle restraints: 10623 sinusoidal: 4452 harmonic: 6171 Sorted by residual: dihedral pdb=" CA ILE C 288 " pdb=" C ILE C 288 " pdb=" N ASN C 289 " pdb=" CA ASN C 289 " ideal model delta harmonic sigma weight residual 180.00 161.34 18.66 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ILE A 288 " pdb=" C ILE A 288 " pdb=" N ASN A 289 " pdb=" CA ASN A 289 " ideal model delta harmonic sigma weight residual 180.00 161.39 18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ILE D 288 " pdb=" C ILE D 288 " pdb=" N ASN D 289 " pdb=" CA ASN D 289 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 10620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1428 0.032 - 0.064: 814 0.064 - 0.096: 201 0.096 - 0.128: 133 0.128 - 0.160: 31 Chirality restraints: 2607 Sorted by residual: chirality pdb=" CA ILE K 75 " pdb=" N ILE K 75 " pdb=" C ILE K 75 " pdb=" CB ILE K 75 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE J 75 " pdb=" N ILE J 75 " pdb=" C ILE J 75 " pdb=" CB ILE J 75 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 2604 not shown) Planarity restraints: 3057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU J 46 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C LEU J 46 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU J 46 " 0.014 2.00e-02 2.50e+03 pdb=" N MET J 47 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 46 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C LEU L 46 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU L 46 " -0.014 2.00e-02 2.50e+03 pdb=" N MET L 47 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 46 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C LEU K 46 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU K 46 " 0.014 2.00e-02 2.50e+03 pdb=" N MET K 47 " 0.012 2.00e-02 2.50e+03 ... (remaining 3054 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 3527 2.78 - 3.31: 15605 3.31 - 3.84: 28858 3.84 - 4.37: 35582 4.37 - 4.90: 62117 Nonbonded interactions: 145689 Sorted by model distance: nonbonded pdb=" O TYR H 59 " pdb=" NH2 ARG L 95 " model vdw 2.255 3.120 nonbonded pdb=" O TYR G 59 " pdb=" NH2 ARG J 95 " model vdw 2.261 3.120 nonbonded pdb=" O TYR I 59 " pdb=" NH2 ARG K 95 " model vdw 2.262 3.120 nonbonded pdb=" OG SER D 270 " pdb=" O PRO D 284 " model vdw 2.384 3.040 nonbonded pdb=" OE1 GLU D 175 " pdb=" NH1 ARG D 262 " model vdw 2.384 3.120 ... (remaining 145684 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 7.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.040 Process input model: 18.230 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17550 Z= 0.203 Angle : 0.686 6.053 23832 Z= 0.355 Chirality : 0.047 0.160 2607 Planarity : 0.004 0.038 3039 Dihedral : 11.525 84.178 6633 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.82 % Allowed : 2.95 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.17), residues: 2130 helix: 1.23 (0.26), residues: 375 sheet: -0.42 (0.26), residues: 447 loop : -0.45 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 170 TYR 0.013 0.002 TYR D 98 PHE 0.019 0.002 PHE F 9 TRP 0.007 0.001 TRP G 103 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00479 (17505) covalent geometry : angle 0.68214 (23721) SS BOND : bond 0.00414 ( 24) SS BOND : angle 0.63643 ( 48) hydrogen bonds : bond 0.19499 ( 683) hydrogen bonds : angle 8.17040 ( 1896) link_BETA1-4 : bond 0.00184 ( 3) link_BETA1-4 : angle 0.94211 ( 9) link_NAG-ASN : bond 0.00366 ( 18) link_NAG-ASN : angle 1.61026 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 454 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 465 average time/residue: 0.5706 time to fit residues: 296.5720 Evaluate side-chains 264 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 261 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain D residue 18 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 25 HIS H 31 ASN L 38 HIS C 192 GLN C 275 HIS E 25 HIS D 159 ASN D 192 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 HIS F 25 HIS I 31 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.170725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.143180 restraints weight = 20570.243| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.80 r_work: 0.3456 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17550 Z= 0.179 Angle : 0.599 5.744 23832 Z= 0.322 Chirality : 0.045 0.163 2607 Planarity : 0.004 0.040 3039 Dihedral : 6.612 58.720 2778 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.44 % Allowed : 12.55 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2130 helix: 1.27 (0.26), residues: 375 sheet: -0.37 (0.24), residues: 471 loop : -0.46 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 109 TYR 0.015 0.002 TYR B 34 PHE 0.019 0.002 PHE D 203 TRP 0.011 0.002 TRP C 127 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00408 (17505) covalent geometry : angle 0.58959 (23721) SS BOND : bond 0.00674 ( 24) SS BOND : angle 1.82875 ( 48) hydrogen bonds : bond 0.04281 ( 683) hydrogen bonds : angle 5.81621 ( 1896) link_BETA1-4 : bond 0.00232 ( 3) link_BETA1-4 : angle 1.11186 ( 9) link_NAG-ASN : bond 0.00450 ( 18) link_NAG-ASN : angle 1.61482 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 285 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8577 (t0) cc_final: 0.8345 (t70) REVERT: L 24 SER cc_start: 0.8126 (OUTLIER) cc_final: 0.7841 (p) REVERT: J 24 SER cc_start: 0.8075 (OUTLIER) cc_final: 0.7767 (p) REVERT: I 46 GLU cc_start: 0.7898 (tt0) cc_final: 0.7582 (tt0) REVERT: I 91 TYR cc_start: 0.8228 (m-80) cc_final: 0.8023 (m-80) REVERT: K 24 SER cc_start: 0.8156 (OUTLIER) cc_final: 0.7883 (p) REVERT: K 72 SER cc_start: 0.8144 (OUTLIER) cc_final: 0.7775 (p) outliers start: 63 outliers final: 28 residues processed: 324 average time/residue: 0.4885 time to fit residues: 180.5784 Evaluate side-chains 280 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 310 LYS Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 90 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 111 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 206 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 275 HIS ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN H 31 ASN ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN G 31 ASN D 226 GLN D 298 HIS ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.168721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142031 restraints weight = 20574.398| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.71 r_work: 0.3420 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17550 Z= 0.249 Angle : 0.627 10.757 23832 Z= 0.332 Chirality : 0.047 0.224 2607 Planarity : 0.004 0.042 3039 Dihedral : 6.427 51.881 2778 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.49 % Allowed : 14.57 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.17), residues: 2130 helix: 1.02 (0.26), residues: 375 sheet: -0.47 (0.23), residues: 492 loop : -0.60 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 109 TYR 0.015 0.002 TYR D 105 PHE 0.022 0.002 PHE A 203 TRP 0.009 0.002 TRP D 127 HIS 0.010 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00580 (17505) covalent geometry : angle 0.61745 (23721) SS BOND : bond 0.00415 ( 24) SS BOND : angle 1.78935 ( 48) hydrogen bonds : bond 0.04306 ( 683) hydrogen bonds : angle 5.67186 ( 1896) link_BETA1-4 : bond 0.00216 ( 3) link_BETA1-4 : angle 1.02536 ( 9) link_NAG-ASN : bond 0.00519 ( 18) link_NAG-ASN : angle 1.67279 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 244 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8660 (pt0) cc_final: 0.8446 (pt0) REVERT: B 77 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8435 (mm) REVERT: B 106 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7961 (mmm160) REVERT: L 24 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7821 (p) REVERT: C 15 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8407 (mp) REVERT: J 24 SER cc_start: 0.8135 (OUTLIER) cc_final: 0.7823 (p) REVERT: F 106 ARG cc_start: 0.8223 (mtp85) cc_final: 0.8013 (mmm160) REVERT: I 46 GLU cc_start: 0.7956 (tt0) cc_final: 0.7726 (tt0) REVERT: K 24 SER cc_start: 0.8137 (OUTLIER) cc_final: 0.7855 (p) outliers start: 64 outliers final: 35 residues processed: 284 average time/residue: 0.4530 time to fit residues: 148.4075 Evaluate side-chains 261 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 310 LYS Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 90 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 104 optimal weight: 8.9990 chunk 142 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 0.0020 chunk 17 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 208 optimal weight: 5.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 38 HIS A 226 GLN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 HIS D 18 HIS D 38 HIS D 166 GLN D 226 GLN ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.173088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.146978 restraints weight = 20472.071| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.71 r_work: 0.3489 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17550 Z= 0.123 Angle : 0.535 8.827 23832 Z= 0.284 Chirality : 0.044 0.206 2607 Planarity : 0.004 0.036 3039 Dihedral : 5.934 52.807 2778 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.89 % Allowed : 16.80 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2130 helix: 1.07 (0.26), residues: 375 sheet: -0.23 (0.25), residues: 459 loop : -0.49 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 71 TYR 0.013 0.001 TYR A 148 PHE 0.011 0.001 PHE A 203 TRP 0.011 0.001 TRP I 98 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00272 (17505) covalent geometry : angle 0.52374 (23721) SS BOND : bond 0.00360 ( 24) SS BOND : angle 1.69721 ( 48) hydrogen bonds : bond 0.03747 ( 683) hydrogen bonds : angle 5.42103 ( 1896) link_BETA1-4 : bond 0.00158 ( 3) link_BETA1-4 : angle 1.01589 ( 9) link_NAG-ASN : bond 0.00424 ( 18) link_NAG-ASN : angle 1.69120 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8377 (mm) REVERT: L 24 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7816 (p) REVERT: C 226 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7571 (mm110) REVERT: J 24 SER cc_start: 0.8108 (OUTLIER) cc_final: 0.7783 (p) REVERT: J 45 LYS cc_start: 0.7693 (tttp) cc_final: 0.7355 (tttt) REVERT: F 17 MET cc_start: 0.8665 (ttp) cc_final: 0.8408 (ttp) REVERT: I 46 GLU cc_start: 0.7939 (tt0) cc_final: 0.7705 (tt0) REVERT: K 24 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7844 (p) REVERT: K 45 LYS cc_start: 0.7737 (tttp) cc_final: 0.7275 (tttt) outliers start: 53 outliers final: 23 residues processed: 282 average time/residue: 0.4687 time to fit residues: 151.8749 Evaluate side-chains 259 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 310 LYS Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 90 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 82 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.172603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.146386 restraints weight = 20332.559| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.71 r_work: 0.3473 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17550 Z= 0.144 Angle : 0.530 6.430 23832 Z= 0.283 Chirality : 0.044 0.241 2607 Planarity : 0.004 0.036 3039 Dihedral : 5.524 53.479 2778 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.16 % Allowed : 16.69 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2130 helix: 1.02 (0.26), residues: 381 sheet: -0.09 (0.23), residues: 504 loop : -0.51 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 38 TYR 0.018 0.001 TYR D 148 PHE 0.015 0.001 PHE C 203 TRP 0.010 0.001 TRP E 92 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00325 (17505) covalent geometry : angle 0.52160 (23721) SS BOND : bond 0.00312 ( 24) SS BOND : angle 1.59099 ( 48) hydrogen bonds : bond 0.03710 ( 683) hydrogen bonds : angle 5.33002 ( 1896) link_BETA1-4 : bond 0.00472 ( 3) link_BETA1-4 : angle 0.85845 ( 9) link_NAG-ASN : bond 0.00500 ( 18) link_NAG-ASN : angle 1.49706 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 231 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: B 77 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8376 (mm) REVERT: H 31 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8247 (m110) REVERT: L 24 SER cc_start: 0.8008 (OUTLIER) cc_final: 0.7762 (p) REVERT: C 224 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8272 (mtp85) REVERT: C 226 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7562 (mm110) REVERT: J 24 SER cc_start: 0.8083 (OUTLIER) cc_final: 0.7785 (p) REVERT: J 45 LYS cc_start: 0.7700 (tttp) cc_final: 0.7395 (tttt) REVERT: I 46 GLU cc_start: 0.7958 (tt0) cc_final: 0.7697 (tt0) REVERT: K 24 SER cc_start: 0.8074 (OUTLIER) cc_final: 0.7819 (p) REVERT: K 45 LYS cc_start: 0.7749 (tttp) cc_final: 0.7309 (tttt) outliers start: 58 outliers final: 33 residues processed: 269 average time/residue: 0.4690 time to fit residues: 145.0756 Evaluate side-chains 256 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 224 ARG Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 310 LYS Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 90 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 165 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 0.0170 chunk 27 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.169461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142531 restraints weight = 20359.942| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.75 r_work: 0.3408 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17550 Z= 0.222 Angle : 0.584 6.630 23832 Z= 0.311 Chirality : 0.045 0.185 2607 Planarity : 0.004 0.037 3039 Dihedral : 5.624 54.370 2778 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.76 % Allowed : 16.69 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.17), residues: 2130 helix: 1.02 (0.26), residues: 375 sheet: -0.30 (0.23), residues: 522 loop : -0.57 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 38 TYR 0.017 0.002 TYR A 148 PHE 0.017 0.002 PHE C 203 TRP 0.008 0.002 TRP I 98 HIS 0.009 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00515 (17505) covalent geometry : angle 0.57463 (23721) SS BOND : bond 0.00361 ( 24) SS BOND : angle 1.86283 ( 48) hydrogen bonds : bond 0.03901 ( 683) hydrogen bonds : angle 5.44416 ( 1896) link_BETA1-4 : bond 0.00280 ( 3) link_BETA1-4 : angle 1.11209 ( 9) link_NAG-ASN : bond 0.00570 ( 18) link_NAG-ASN : angle 1.42904 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 227 time to evaluate : 0.569 Fit side-chains REVERT: B 77 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8449 (mm) REVERT: B 106 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7909 (mmm160) REVERT: L 24 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7820 (p) REVERT: C 15 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8446 (mp) REVERT: J 24 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7822 (p) REVERT: J 45 LYS cc_start: 0.7702 (tttp) cc_final: 0.7400 (tttt) REVERT: I 5 VAL cc_start: 0.7637 (OUTLIER) cc_final: 0.7408 (p) REVERT: I 51 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7745 (tp) REVERT: K 24 SER cc_start: 0.8105 (OUTLIER) cc_final: 0.7831 (p) REVERT: K 45 LYS cc_start: 0.7721 (tttp) cc_final: 0.7223 (tttt) outliers start: 69 outliers final: 38 residues processed: 271 average time/residue: 0.4352 time to fit residues: 136.0933 Evaluate side-chains 260 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 310 LYS Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 90 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 194 optimal weight: 0.0050 chunk 60 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.172128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.145980 restraints weight = 20156.662| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.72 r_work: 0.3478 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17550 Z= 0.137 Angle : 0.533 6.501 23832 Z= 0.286 Chirality : 0.043 0.166 2607 Planarity : 0.004 0.034 3039 Dihedral : 5.299 55.119 2778 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.22 % Allowed : 17.68 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2130 helix: 1.19 (0.26), residues: 375 sheet: -0.24 (0.23), residues: 522 loop : -0.50 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 38 TYR 0.014 0.001 TYR D 105 PHE 0.012 0.001 PHE C 203 TRP 0.011 0.001 TRP I 98 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00307 (17505) covalent geometry : angle 0.52587 (23721) SS BOND : bond 0.00254 ( 24) SS BOND : angle 1.50168 ( 48) hydrogen bonds : bond 0.03651 ( 683) hydrogen bonds : angle 5.27008 ( 1896) link_BETA1-4 : bond 0.00338 ( 3) link_BETA1-4 : angle 0.99777 ( 9) link_NAG-ASN : bond 0.00464 ( 18) link_NAG-ASN : angle 1.37744 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 235 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: B 77 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8395 (mm) REVERT: B 106 ARG cc_start: 0.8044 (mtp85) cc_final: 0.7832 (mmm160) REVERT: H 5 VAL cc_start: 0.7580 (OUTLIER) cc_final: 0.7355 (p) REVERT: L 24 SER cc_start: 0.8042 (OUTLIER) cc_final: 0.7770 (p) REVERT: L 45 LYS cc_start: 0.7620 (ttmt) cc_final: 0.7226 (tttt) REVERT: C 224 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8301 (mtp85) REVERT: G 5 VAL cc_start: 0.7491 (OUTLIER) cc_final: 0.7285 (p) REVERT: J 24 SER cc_start: 0.8108 (OUTLIER) cc_final: 0.7785 (p) REVERT: I 5 VAL cc_start: 0.7545 (OUTLIER) cc_final: 0.7309 (p) REVERT: I 91 TYR cc_start: 0.8223 (m-80) cc_final: 0.8019 (m-80) REVERT: K 24 SER cc_start: 0.8100 (OUTLIER) cc_final: 0.7830 (p) REVERT: K 45 LYS cc_start: 0.7660 (tttp) cc_final: 0.7181 (tttt) outliers start: 59 outliers final: 35 residues processed: 275 average time/residue: 0.4795 time to fit residues: 151.5394 Evaluate side-chains 253 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 224 ARG Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 310 LYS Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 90 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 25 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 226 GLN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.171647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145160 restraints weight = 20344.391| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.73 r_work: 0.3457 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17550 Z= 0.160 Angle : 0.550 7.479 23832 Z= 0.293 Chirality : 0.044 0.163 2607 Planarity : 0.004 0.034 3039 Dihedral : 5.144 55.764 2776 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.16 % Allowed : 18.17 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2130 helix: 1.23 (0.26), residues: 375 sheet: -0.25 (0.23), residues: 522 loop : -0.48 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 106 TYR 0.023 0.001 TYR D 148 PHE 0.013 0.002 PHE C 203 TRP 0.010 0.001 TRP I 98 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00366 (17505) covalent geometry : angle 0.54251 (23721) SS BOND : bond 0.00279 ( 24) SS BOND : angle 1.54306 ( 48) hydrogen bonds : bond 0.03713 ( 683) hydrogen bonds : angle 5.24245 ( 1896) link_BETA1-4 : bond 0.00259 ( 3) link_BETA1-4 : angle 0.98853 ( 9) link_NAG-ASN : bond 0.00485 ( 18) link_NAG-ASN : angle 1.37542 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 0.676 Fit side-chains REVERT: B 77 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8394 (mm) REVERT: B 106 ARG cc_start: 0.8109 (mtp85) cc_final: 0.7853 (mmm160) REVERT: H 5 VAL cc_start: 0.7463 (OUTLIER) cc_final: 0.7243 (p) REVERT: L 24 SER cc_start: 0.8015 (OUTLIER) cc_final: 0.7741 (p) REVERT: L 45 LYS cc_start: 0.7682 (ttmt) cc_final: 0.7340 (tttt) REVERT: C 15 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8442 (mp) REVERT: C 224 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8340 (mtp85) REVERT: G 5 VAL cc_start: 0.7422 (OUTLIER) cc_final: 0.7207 (p) REVERT: G 79 TYR cc_start: 0.7716 (m-80) cc_final: 0.7410 (m-80) REVERT: J 24 SER cc_start: 0.8081 (OUTLIER) cc_final: 0.7763 (p) REVERT: J 45 LYS cc_start: 0.7597 (tttp) cc_final: 0.7365 (pttt) REVERT: I 5 VAL cc_start: 0.7637 (OUTLIER) cc_final: 0.7397 (p) REVERT: K 24 SER cc_start: 0.8070 (OUTLIER) cc_final: 0.7792 (p) REVERT: K 45 LYS cc_start: 0.7739 (tttp) cc_final: 0.7279 (tttt) outliers start: 58 outliers final: 38 residues processed: 254 average time/residue: 0.4777 time to fit residues: 139.5593 Evaluate side-chains 253 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 224 ARG Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 310 LYS Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 90 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 69 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 152 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 38 optimal weight: 0.0570 chunk 71 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 25 HIS ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.172135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.145795 restraints weight = 20358.529| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.73 r_work: 0.3468 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17550 Z= 0.155 Angle : 0.546 7.754 23832 Z= 0.292 Chirality : 0.044 0.183 2607 Planarity : 0.004 0.034 3039 Dihedral : 5.061 56.482 2776 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.11 % Allowed : 18.66 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.18), residues: 2130 helix: 1.30 (0.26), residues: 375 sheet: -0.26 (0.23), residues: 522 loop : -0.48 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 106 TYR 0.017 0.001 TYR D 105 PHE 0.012 0.002 PHE C 203 TRP 0.009 0.001 TRP G 98 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00352 (17505) covalent geometry : angle 0.53909 (23721) SS BOND : bond 0.00275 ( 24) SS BOND : angle 1.47529 ( 48) hydrogen bonds : bond 0.03680 ( 683) hydrogen bonds : angle 5.20201 ( 1896) link_BETA1-4 : bond 0.00303 ( 3) link_BETA1-4 : angle 1.02741 ( 9) link_NAG-ASN : bond 0.00473 ( 18) link_NAG-ASN : angle 1.38310 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 0.662 Fit side-chains REVERT: B 77 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8385 (mm) REVERT: B 106 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7864 (mmm160) REVERT: L 24 SER cc_start: 0.7997 (OUTLIER) cc_final: 0.7710 (p) REVERT: L 45 LYS cc_start: 0.7581 (ttmt) cc_final: 0.7311 (tttt) REVERT: C 224 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8270 (mtp85) REVERT: G 5 VAL cc_start: 0.7424 (OUTLIER) cc_final: 0.7216 (p) REVERT: G 57 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6082 (mt-10) REVERT: G 79 TYR cc_start: 0.7715 (m-80) cc_final: 0.7474 (m-80) REVERT: J 24 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7730 (p) REVERT: J 45 LYS cc_start: 0.7599 (tttp) cc_final: 0.7373 (pttt) REVERT: K 22 SER cc_start: 0.8380 (t) cc_final: 0.7945 (p) REVERT: K 24 SER cc_start: 0.8065 (OUTLIER) cc_final: 0.7763 (p) REVERT: K 45 LYS cc_start: 0.7722 (tttp) cc_final: 0.7260 (tttt) outliers start: 57 outliers final: 38 residues processed: 258 average time/residue: 0.4439 time to fit residues: 132.6058 Evaluate side-chains 256 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 224 ARG Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 310 LYS Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 90 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 100 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 186 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 25 HIS ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.173607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.147509 restraints weight = 20135.476| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.73 r_work: 0.3489 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17550 Z= 0.130 Angle : 0.527 7.620 23832 Z= 0.282 Chirality : 0.043 0.170 2607 Planarity : 0.004 0.033 3039 Dihedral : 4.887 57.027 2776 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.89 % Allowed : 19.26 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.18), residues: 2130 helix: 1.38 (0.26), residues: 375 sheet: -0.08 (0.24), residues: 504 loop : -0.49 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 76 TYR 0.016 0.001 TYR C 105 PHE 0.010 0.001 PHE C 203 TRP 0.011 0.001 TRP I 98 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00292 (17505) covalent geometry : angle 0.52019 (23721) SS BOND : bond 0.00249 ( 24) SS BOND : angle 1.41140 ( 48) hydrogen bonds : bond 0.03604 ( 683) hydrogen bonds : angle 5.11076 ( 1896) link_BETA1-4 : bond 0.00325 ( 3) link_BETA1-4 : angle 1.02592 ( 9) link_NAG-ASN : bond 0.00439 ( 18) link_NAG-ASN : angle 1.36715 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 236 time to evaluate : 0.676 Fit side-chains REVERT: B 32 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7857 (m) REVERT: B 77 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8381 (mm) REVERT: B 106 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7778 (mmm160) REVERT: L 24 SER cc_start: 0.7983 (OUTLIER) cc_final: 0.7713 (p) REVERT: L 45 LYS cc_start: 0.7451 (ttmt) cc_final: 0.7190 (tttt) REVERT: C 224 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8232 (mtp85) REVERT: G 5 VAL cc_start: 0.7339 (OUTLIER) cc_final: 0.7137 (p) REVERT: G 79 TYR cc_start: 0.7619 (m-80) cc_final: 0.7397 (m-80) REVERT: J 22 SER cc_start: 0.8362 (t) cc_final: 0.7916 (p) REVERT: J 24 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7738 (p) REVERT: I 5 VAL cc_start: 0.7498 (OUTLIER) cc_final: 0.7268 (p) REVERT: I 91 TYR cc_start: 0.8331 (m-80) cc_final: 0.7786 (m-80) REVERT: K 22 SER cc_start: 0.8367 (t) cc_final: 0.7917 (p) REVERT: K 24 SER cc_start: 0.8038 (OUTLIER) cc_final: 0.7741 (p) REVERT: K 45 LYS cc_start: 0.7623 (tttp) cc_final: 0.7130 (tttt) outliers start: 53 outliers final: 34 residues processed: 274 average time/residue: 0.4307 time to fit residues: 137.7556 Evaluate side-chains 264 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 224 ARG Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 310 LYS Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 90 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 10 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 25 HIS H 31 ASN C 197 ASN ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.171897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.145953 restraints weight = 20354.262| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.71 r_work: 0.3447 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17550 Z= 0.173 Angle : 0.561 10.613 23832 Z= 0.299 Chirality : 0.044 0.165 2607 Planarity : 0.004 0.036 3039 Dihedral : 5.028 57.390 2776 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.67 % Allowed : 19.97 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.18), residues: 2130 helix: 1.36 (0.26), residues: 375 sheet: -0.15 (0.23), residues: 504 loop : -0.54 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 109 TYR 0.017 0.002 TYR D 105 PHE 0.017 0.002 PHE I 67 TRP 0.008 0.001 TRP G 36 HIS 0.008 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00396 (17505) covalent geometry : angle 0.55433 (23721) SS BOND : bond 0.00286 ( 24) SS BOND : angle 1.49629 ( 48) hydrogen bonds : bond 0.03739 ( 683) hydrogen bonds : angle 5.17694 ( 1896) link_BETA1-4 : bond 0.00297 ( 3) link_BETA1-4 : angle 1.06283 ( 9) link_NAG-ASN : bond 0.00475 ( 18) link_NAG-ASN : angle 1.40448 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6035.96 seconds wall clock time: 103 minutes 47.07 seconds (6227.07 seconds total)