Starting phenix.real_space_refine on Tue Aug 26 18:30:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5n6w_3595/08_2025/5n6w_3595.cif Found real_map, /net/cci-nas-00/data/ceres_data/5n6w_3595/08_2025/5n6w_3595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5n6w_3595/08_2025/5n6w_3595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5n6w_3595/08_2025/5n6w_3595.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5n6w_3595/08_2025/5n6w_3595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5n6w_3595/08_2025/5n6w_3595.map" } resolution = 4.2 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= 0.004 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: 5 Type Number sf(0) Gaussians S 112 5.16 5 C 13216 2.51 5 N 3600 2.21 5 O 3792 1.98 5 H 20032 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 160 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40752 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "C" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "D" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "E" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "F" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "G" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "H" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "I" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "J" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "K" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "L" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "M" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "N" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "O" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "P" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2547 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Time building chain proxies: 6.57, per 1000 atoms: 0.16 Number of scatterers: 40752 At special positions: 0 Unit cell: (145.77, 145.77, 86.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 O 3792 8.00 N 3600 7.00 C 13216 6.00 H 20032 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 219 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 219 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 219 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 219 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 219 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 219 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 219 " distance=2.03 Simple disulfide: pdb=" SG CYS I 63 " - pdb=" SG CYS I 219 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 219 " distance=2.03 Simple disulfide: pdb=" SG CYS K 63 " - pdb=" SG CYS K 219 " distance=2.03 Simple disulfide: pdb=" SG CYS L 63 " - pdb=" SG CYS L 219 " distance=2.03 Simple disulfide: pdb=" SG CYS M 63 " - pdb=" SG CYS M 219 " distance=2.03 Simple disulfide: pdb=" SG CYS N 63 " - pdb=" SG CYS N 219 " distance=2.03 Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 219 " distance=2.03 Simple disulfide: pdb=" SG CYS P 63 " - pdb=" SG CYS P 219 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 32 sheets defined 0.0% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 196 removed outlier: 3.922A pdb=" N ILE A 194 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 196 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU A 217 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 164 removed outlier: 3.889A pdb=" N TRP A 163 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 155 " --> pdb=" O TRP A 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 200 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 156 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE A 198 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 194 through 196 removed outlier: 3.921A pdb=" N ILE B 194 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 196 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU B 217 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 163 through 164 removed outlier: 3.890A pdb=" N TRP B 163 " --> pdb=" O TYR B 155 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 155 " --> pdb=" O TRP B 163 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 200 " --> pdb=" O GLN B 154 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B 156 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE B 198 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 194 through 196 removed outlier: 3.920A pdb=" N ILE C 194 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 196 " --> pdb=" O LYS C 131 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU C 217 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 163 through 164 removed outlier: 3.890A pdb=" N TRP C 163 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR C 155 " --> pdb=" O TRP C 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 200 " --> pdb=" O GLN C 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG C 156 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE C 198 " --> pdb=" O ARG C 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 194 through 196 removed outlier: 3.921A pdb=" N ILE D 194 " --> pdb=" O ILE D 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 196 " --> pdb=" O LYS D 131 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU D 217 " --> pdb=" O SER D 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 163 through 164 removed outlier: 3.891A pdb=" N TRP D 163 " --> pdb=" O TYR D 155 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR D 155 " --> pdb=" O TRP D 163 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 200 " --> pdb=" O GLN D 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG D 156 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE D 198 " --> pdb=" O ARG D 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 194 through 196 removed outlier: 3.927A pdb=" N ILE E 194 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER E 196 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU E 217 " --> pdb=" O SER E 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 163 through 164 removed outlier: 3.886A pdb=" N TRP E 163 " --> pdb=" O TYR E 155 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR E 155 " --> pdb=" O TRP E 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG E 200 " --> pdb=" O GLN E 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG E 156 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE E 198 " --> pdb=" O ARG E 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 194 through 196 removed outlier: 3.921A pdb=" N ILE F 194 " --> pdb=" O ILE F 133 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER F 196 " --> pdb=" O LYS F 131 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU F 217 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 163 through 164 removed outlier: 3.905A pdb=" N TRP F 163 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR F 155 " --> pdb=" O TRP F 163 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG F 200 " --> pdb=" O GLN F 154 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG F 156 " --> pdb=" O PHE F 198 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE F 198 " --> pdb=" O ARG F 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 194 through 196 removed outlier: 3.923A pdb=" N ILE G 194 " --> pdb=" O ILE G 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER G 196 " --> pdb=" O LYS G 131 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU G 217 " --> pdb=" O SER G 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 163 through 164 removed outlier: 3.891A pdb=" N TRP G 163 " --> pdb=" O TYR G 155 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR G 155 " --> pdb=" O TRP G 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG G 200 " --> pdb=" O GLN G 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG G 156 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE G 198 " --> pdb=" O ARG G 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 194 through 196 removed outlier: 3.923A pdb=" N ILE H 194 " --> pdb=" O ILE H 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER H 196 " --> pdb=" O LYS H 131 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU H 217 " --> pdb=" O SER H 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 163 through 164 removed outlier: 3.890A pdb=" N TRP H 163 " --> pdb=" O TYR H 155 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR H 155 " --> pdb=" O TRP H 163 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG H 200 " --> pdb=" O GLN H 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG H 156 " --> pdb=" O PHE H 198 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE H 198 " --> pdb=" O ARG H 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 194 through 196 removed outlier: 3.920A pdb=" N ILE I 194 " --> pdb=" O ILE I 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER I 196 " --> pdb=" O LYS I 131 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU I 217 " --> pdb=" O SER I 134 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 163 through 164 removed outlier: 3.889A pdb=" N TRP I 163 " --> pdb=" O TYR I 155 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR I 155 " --> pdb=" O TRP I 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG I 200 " --> pdb=" O GLN I 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG I 156 " --> pdb=" O PHE I 198 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE I 198 " --> pdb=" O ARG I 156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 194 through 196 removed outlier: 3.921A pdb=" N ILE J 194 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER J 196 " --> pdb=" O LYS J 131 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU J 217 " --> pdb=" O SER J 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 163 through 164 removed outlier: 3.893A pdb=" N TRP J 163 " --> pdb=" O TYR J 155 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR J 155 " --> pdb=" O TRP J 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG J 200 " --> pdb=" O GLN J 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG J 156 " --> pdb=" O PHE J 198 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE J 198 " --> pdb=" O ARG J 156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 194 through 196 removed outlier: 3.921A pdb=" N ILE K 194 " --> pdb=" O ILE K 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER K 196 " --> pdb=" O LYS K 131 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU K 217 " --> pdb=" O SER K 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 163 through 164 removed outlier: 3.890A pdb=" N TRP K 163 " --> pdb=" O TYR K 155 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR K 155 " --> pdb=" O TRP K 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG K 200 " --> pdb=" O GLN K 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG K 156 " --> pdb=" O PHE K 198 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE K 198 " --> pdb=" O ARG K 156 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 194 through 196 removed outlier: 3.921A pdb=" N ILE L 194 " --> pdb=" O ILE L 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER L 196 " --> pdb=" O LYS L 131 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU L 217 " --> pdb=" O SER L 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 163 through 164 removed outlier: 3.889A pdb=" N TRP L 163 " --> pdb=" O TYR L 155 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR L 155 " --> pdb=" O TRP L 163 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG L 200 " --> pdb=" O GLN L 154 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG L 156 " --> pdb=" O PHE L 198 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE L 198 " --> pdb=" O ARG L 156 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 194 through 196 removed outlier: 3.922A pdb=" N ILE M 194 " --> pdb=" O ILE M 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER M 196 " --> pdb=" O LYS M 131 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU M 217 " --> pdb=" O SER M 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 163 through 164 removed outlier: 3.905A pdb=" N TRP M 163 " --> pdb=" O TYR M 155 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR M 155 " --> pdb=" O TRP M 163 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG M 200 " --> pdb=" O GLN M 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG M 156 " --> pdb=" O PHE M 198 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE M 198 " --> pdb=" O ARG M 156 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 194 through 196 removed outlier: 3.923A pdb=" N ILE N 194 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER N 196 " --> pdb=" O LYS N 131 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU N 217 " --> pdb=" O SER N 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 163 through 164 removed outlier: 3.906A pdb=" N TRP N 163 " --> pdb=" O TYR N 155 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR N 155 " --> pdb=" O TRP N 163 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG N 200 " --> pdb=" O GLN N 154 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG N 156 " --> pdb=" O PHE N 198 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE N 198 " --> pdb=" O ARG N 156 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 194 through 196 removed outlier: 3.921A pdb=" N ILE O 194 " --> pdb=" O ILE O 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER O 196 " --> pdb=" O LYS O 131 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU O 217 " --> pdb=" O SER O 134 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 163 through 164 removed outlier: 3.890A pdb=" N TRP O 163 " --> pdb=" O TYR O 155 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR O 155 " --> pdb=" O TRP O 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG O 200 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG O 156 " --> pdb=" O PHE O 198 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE O 198 " --> pdb=" O ARG O 156 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 194 through 196 removed outlier: 3.918A pdb=" N ILE P 194 " --> pdb=" O ILE P 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER P 196 " --> pdb=" O LYS P 131 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU P 217 " --> pdb=" O SER P 134 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 163 through 164 removed outlier: 3.897A pdb=" N TRP P 163 " --> pdb=" O TYR P 155 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR P 155 " --> pdb=" O TRP P 163 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG P 200 " --> pdb=" O GLN P 154 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG P 156 " --> pdb=" O PHE P 198 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE P 198 " --> pdb=" O ARG P 156 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 144 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: 8.34 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19984 1.03 - 1.23: 80 1.23 - 1.42: 9376 1.42 - 1.62: 11744 1.62 - 1.81: 144 Bond restraints: 41328 Sorted by residual: bond pdb=" N GLY I 140 " pdb=" CA GLY I 140 " ideal model delta sigma weight residual 1.445 1.452 -0.007 8.30e-03 1.45e+04 7.43e-01 bond pdb=" N GLY H 140 " pdb=" CA GLY H 140 " ideal model delta sigma weight residual 1.445 1.452 -0.007 8.30e-03 1.45e+04 7.33e-01 bond pdb=" N GLY N 140 " pdb=" CA GLY N 140 " ideal model delta sigma weight residual 1.445 1.452 -0.007 8.30e-03 1.45e+04 7.09e-01 bond pdb=" N GLY P 140 " pdb=" CA GLY P 140 " ideal model delta sigma weight residual 1.445 1.451 -0.007 8.30e-03 1.45e+04 6.62e-01 bond pdb=" N GLY M 140 " pdb=" CA GLY M 140 " ideal model delta sigma weight residual 1.445 1.451 -0.007 8.30e-03 1.45e+04 6.47e-01 ... (remaining 41323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.73: 67339 0.73 - 1.45: 6378 1.45 - 2.18: 435 2.18 - 2.90: 53 2.90 - 3.63: 83 Bond angle restraints: 74288 Sorted by residual: angle pdb=" N TRP C 92 " pdb=" CA TRP C 92 " pdb=" C TRP C 92 " ideal model delta sigma weight residual 114.56 110.93 3.63 1.27e+00 6.20e-01 8.15e+00 angle pdb=" N TRP E 92 " pdb=" CA TRP E 92 " pdb=" C TRP E 92 " ideal model delta sigma weight residual 114.56 110.93 3.63 1.27e+00 6.20e-01 8.15e+00 angle pdb=" N TRP H 92 " pdb=" CA TRP H 92 " pdb=" C TRP H 92 " ideal model delta sigma weight residual 114.56 110.94 3.62 1.27e+00 6.20e-01 8.14e+00 angle pdb=" N TRP L 92 " pdb=" CA TRP L 92 " pdb=" C TRP L 92 " ideal model delta sigma weight residual 114.56 110.96 3.60 1.27e+00 6.20e-01 8.03e+00 angle pdb=" N TRP P 92 " pdb=" CA TRP P 92 " pdb=" C TRP P 92 " ideal model delta sigma weight residual 114.56 110.97 3.59 1.27e+00 6.20e-01 8.00e+00 ... (remaining 74283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.61: 18272 10.61 - 21.22: 768 21.22 - 31.83: 253 31.83 - 42.44: 115 42.44 - 53.05: 112 Dihedral angle restraints: 19520 sinusoidal: 10464 harmonic: 9056 Sorted by residual: dihedral pdb=" SG CYS H 63 " pdb=" CB CYS H 219 " pdb=" SG CYS H 219 " pdb=" CA CYS H 219 " ideal model delta sinusoidal sigma weight residual -73.00 -117.66 44.66 1 2.00e+01 2.50e-03 6.93e+00 dihedral pdb=" SG CYS E 63 " pdb=" CB CYS E 219 " pdb=" SG CYS E 219 " pdb=" CA CYS E 219 " ideal model delta sinusoidal sigma weight residual -73.00 -117.65 44.65 1 2.00e+01 2.50e-03 6.93e+00 dihedral pdb=" SG CYS A 63 " pdb=" CB CYS A 219 " pdb=" SG CYS A 219 " pdb=" CA CYS A 219 " ideal model delta sinusoidal sigma weight residual -73.00 -117.64 44.64 1 2.00e+01 2.50e-03 6.92e+00 ... (remaining 19517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1919 0.026 - 0.052: 717 0.052 - 0.079: 68 0.079 - 0.105: 172 0.105 - 0.131: 148 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CA ILE E 125 " pdb=" N ILE E 125 " pdb=" C ILE E 125 " pdb=" CB ILE E 125 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE D 125 " pdb=" N ILE D 125 " pdb=" C ILE D 125 " pdb=" CB ILE D 125 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE O 125 " pdb=" N ILE O 125 " pdb=" C ILE O 125 " pdb=" CB ILE O 125 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 3021 not shown) Planarity restraints: 6064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN G 187 " 0.142 2.00e-02 2.50e+03 1.59e-01 3.81e+02 pdb=" CD GLN G 187 " -0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN G 187 " -0.139 2.00e-02 2.50e+03 pdb=" NE2 GLN G 187 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN G 187 " -0.236 2.00e-02 2.50e+03 pdb="HE22 GLN G 187 " 0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN L 187 " 0.142 2.00e-02 2.50e+03 1.59e-01 3.80e+02 pdb=" CD GLN L 187 " -0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN L 187 " -0.139 2.00e-02 2.50e+03 pdb=" NE2 GLN L 187 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN L 187 " -0.236 2.00e-02 2.50e+03 pdb="HE22 GLN L 187 " 0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 187 " 0.142 2.00e-02 2.50e+03 1.59e-01 3.80e+02 pdb=" CD GLN D 187 " -0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN D 187 " -0.139 2.00e-02 2.50e+03 pdb=" NE2 GLN D 187 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN D 187 " -0.236 2.00e-02 2.50e+03 pdb="HE22 GLN D 187 " 0.239 2.00e-02 2.50e+03 ... (remaining 6061 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 6348 2.30 - 2.87: 91425 2.87 - 3.45: 91171 3.45 - 4.02: 124081 4.02 - 4.60: 190048 Nonbonded interactions: 503073 Sorted by model distance: nonbonded pdb=" O ALA E 98 " pdb=" HE ARG E 102 " model vdw 1.720 2.450 nonbonded pdb=" O ALA H 98 " pdb=" HE ARG H 102 " model vdw 1.721 2.450 nonbonded pdb=" O ALA M 98 " pdb=" HE ARG M 102 " model vdw 1.721 2.450 nonbonded pdb=" O ALA C 98 " pdb=" HE ARG C 102 " model vdw 1.721 2.450 nonbonded pdb=" O ALA P 98 " pdb=" HE ARG P 102 " model vdw 1.721 2.450 ... (remaining 503068 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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 group one per residue 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.240 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 33.680 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2845 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 : 0.001 0.013 21312 Z= 0.090 Angle : 0.360 3.625 28960 Z= 0.217 Chirality : 0.041 0.131 3024 Planarity : 0.001 0.011 3680 Dihedral : 4.916 31.060 7792 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 2.58 % Allowed : 17.70 % Favored : 79.72 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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 aren not related in a simple way. whole: -5.61 (0.12), residues: 2480 helix: None (None), residues: 0 sheet: -4.79 (0.17), residues: 160 loop : -4.14 (0.10), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 213 TYR 0.003 0.000 TYR N 166 PHE 0.001 0.000 PHE K 116 TRP 0.001 0.000 TRP K 163 HIS 0.001 0.000 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00149 (21296) covalent geometry : angle 0.35986 (28928) SS BOND : bond 0.00053 ( 16) SS BOND : angle 0.26254 ( 32) hydrogen bonds : bond 0.30526 ( 64) hydrogen bonds : angle 5.94908 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 782 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 782 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 ILE cc_start: 0.6763 (mt) cc_final: 0.4917 (mt) REVERT: C 130 ILE cc_start: 0.6615 (mt) cc_final: 0.4747 (mt) REVERT: D 130 ILE cc_start: 0.6388 (mt) cc_final: 0.4521 (mt) REVERT: D 199 ILE cc_start: 0.6200 (mt) cc_final: 0.5950 (mt) REVERT: E 121 GLN cc_start: 0.6261 (tp40) cc_final: 0.5864 (tm-30) REVERT: J 199 ILE cc_start: 0.6404 (mt) cc_final: 0.6194 (mt) REVERT: P 212 ILE cc_start: 0.3049 (tt) cc_final: 0.2799 (tt) outliers start: 0 outliers final: 0 residues processed: 782 average time/residue: 0.4236 time to fit residues: 469.8067 Evaluate side-chains 551 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 551 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN B 187 GLN C 187 GLN D 187 GLN E 187 GLN F 187 GLN G 187 GLN H 187 GLN I 187 GLN J 187 GLN K 187 GLN L 187 GLN M 187 GLN N 187 GLN O 187 GLN P 187 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5177 r_free = 0.5177 target = 0.232582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.196293 restraints weight = 133271.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.202668 restraints weight = 92830.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.207571 restraints weight = 68734.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.211456 restraints weight = 53251.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.214557 restraints weight = 42640.685| |-----------------------------------------------------------------------------| r_work (final): 0.5040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5418 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21312 Z= 0.158 Angle : 0.526 4.875 28960 Z= 0.272 Chirality : 0.042 0.151 3024 Planarity : 0.005 0.053 3680 Dihedral : 3.014 16.190 2784 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 1.29 % Allowed : 9.23 % Favored : 89.48 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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 aren not related in a simple way. whole: -4.82 (0.13), residues: 2480 helix: None (None), residues: 0 sheet: -3.18 (0.18), residues: 224 loop : -3.61 (0.11), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 200 TYR 0.011 0.001 TYR J 155 PHE 0.009 0.001 PHE K 198 TRP 0.010 0.001 TRP H 147 HIS 0.003 0.001 HIS G 141 Details of bonding type rmsd covalent geometry : bond 0.00347 (21296) covalent geometry : angle 0.52571 (28928) SS BOND : bond 0.00305 ( 16) SS BOND : angle 0.37509 ( 32) hydrogen bonds : bond 0.02670 ( 64) hydrogen bonds : angle 4.44920 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 637 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 637 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.7830 (mt) cc_final: 0.7478 (tt) REVERT: B 117 GLN cc_start: 0.8077 (mt0) cc_final: 0.7826 (pp30) REVERT: B 215 GLU cc_start: 0.5037 (mm-30) cc_final: 0.3862 (mp0) REVERT: D 215 GLU cc_start: 0.4905 (mm-30) cc_final: 0.3827 (mp0) REVERT: E 215 GLU cc_start: 0.4880 (mm-30) cc_final: 0.3396 (mp0) REVERT: F 69 LEU cc_start: 0.5742 (mt) cc_final: 0.5436 (tt) REVERT: F 215 GLU cc_start: 0.4738 (mm-30) cc_final: 0.3673 (mp0) REVERT: G 215 GLU cc_start: 0.6061 (tp30) cc_final: 0.4939 (mp0) REVERT: H 215 GLU cc_start: 0.5869 (tp30) cc_final: 0.4294 (mp0) REVERT: I 209 ARG cc_start: 0.7975 (mtm110) cc_final: 0.7719 (mtm110) REVERT: K 121 GLN cc_start: 0.8142 (tp40) cc_final: 0.7497 (tm-30) REVERT: K 145 ASP cc_start: 0.7819 (m-30) cc_final: 0.7387 (t0) REVERT: K 215 GLU cc_start: 0.5315 (mm-30) cc_final: 0.4086 (mp0) REVERT: L 121 GLN cc_start: 0.7993 (tp40) cc_final: 0.6765 (tm-30) REVERT: M 121 GLN cc_start: 0.8354 (tp40) cc_final: 0.7635 (tm-30) REVERT: M 145 ASP cc_start: 0.7738 (m-30) cc_final: 0.7348 (t0) REVERT: M 215 GLU cc_start: 0.6698 (tp30) cc_final: 0.6136 (mp0) REVERT: N 126 ASP cc_start: 0.7909 (t0) cc_final: 0.7708 (t0) REVERT: N 215 GLU cc_start: 0.6305 (tp30) cc_final: 0.5638 (mp0) REVERT: O 145 ASP cc_start: 0.7459 (m-30) cc_final: 0.6731 (t0) REVERT: P 215 GLU cc_start: 0.6018 (tp30) cc_final: 0.5669 (mp0) outliers start: 0 outliers final: 0 residues processed: 637 average time/residue: 0.4356 time to fit residues: 393.9638 Evaluate side-chains 498 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 118 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN G 85 ASN ** H 207 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 = 0.4906 r_free = 0.4906 target = 0.203649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.168228 restraints weight = 155909.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.173024 restraints weight = 112506.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.176804 restraints weight = 87365.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.179618 restraints weight = 71522.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.181803 restraints weight = 61073.856| |-----------------------------------------------------------------------------| r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.8013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 21312 Z= 0.268 Angle : 0.762 9.433 28960 Z= 0.403 Chirality : 0.046 0.162 3024 Planarity : 0.007 0.151 3680 Dihedral : 4.964 18.178 2784 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.85 % Allowed : 13.39 % Favored : 85.77 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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 aren not related in a simple way. whole: -4.44 (0.13), residues: 2480 helix: None (None), residues: 0 sheet: -1.16 (0.21), residues: 160 loop : -3.50 (0.11), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG L 209 TYR 0.027 0.002 TYR H 155 PHE 0.016 0.003 PHE J 198 TRP 0.022 0.003 TRP F 122 HIS 0.016 0.002 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00577 (21296) covalent geometry : angle 0.76129 (28928) SS BOND : bond 0.00727 ( 16) SS BOND : angle 1.41486 ( 32) hydrogen bonds : bond 0.01815 ( 64) hydrogen bonds : angle 5.48758 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 685 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 685 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 ILE cc_start: 0.8118 (mt) cc_final: 0.7809 (mm) REVERT: C 214 MET cc_start: 0.7087 (tmm) cc_final: 0.6872 (tmm) REVERT: E 121 GLN cc_start: 0.8064 (tp40) cc_final: 0.7153 (tm-30) REVERT: E 125 ILE cc_start: 0.8299 (mt) cc_final: 0.7986 (mm) REVERT: F 124 GLN cc_start: 0.6828 (tp-100) cc_final: 0.6540 (tm-30) REVERT: G 145 ASP cc_start: 0.8119 (m-30) cc_final: 0.7910 (t0) REVERT: L 121 GLN cc_start: 0.8111 (tp40) cc_final: 0.6777 (tm-30) REVERT: L 167 LYS cc_start: 0.7665 (mtmt) cc_final: 0.7321 (mttp) REVERT: N 215 GLU cc_start: 0.5812 (tp30) cc_final: 0.4814 (tp30) outliers start: 0 outliers final: 0 residues processed: 685 average time/residue: 0.3836 time to fit residues: 384.7318 Evaluate side-chains 548 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 548 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 166 optimal weight: 0.7980 chunk 206 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 207 HIS J 124 GLN ** L 80 GLN ** 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 = 0.4899 r_free = 0.4899 target = 0.200978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.164422 restraints weight = 149918.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.169430 restraints weight = 104873.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.173273 restraints weight = 79953.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.176125 restraints weight = 64795.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.178377 restraints weight = 55008.367| |-----------------------------------------------------------------------------| r_work (final): 0.4689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.9075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21312 Z= 0.156 Angle : 0.533 4.604 28960 Z= 0.277 Chirality : 0.042 0.161 3024 Planarity : 0.005 0.058 3680 Dihedral : 4.411 17.229 2784 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.65 % Allowed : 11.37 % Favored : 87.98 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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 aren not related in a simple way. whole: -4.13 (0.14), residues: 2480 helix: None (None), residues: 0 sheet: -1.28 (0.25), residues: 224 loop : -3.28 (0.11), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 197 TYR 0.012 0.001 TYR K 155 PHE 0.010 0.001 PHE H 176 TRP 0.016 0.002 TRP J 112 HIS 0.005 0.001 HIS O 207 Details of bonding type rmsd covalent geometry : bond 0.00329 (21296) covalent geometry : angle 0.53242 (28928) SS BOND : bond 0.00462 ( 16) SS BOND : angle 0.68101 ( 32) hydrogen bonds : bond 0.01381 ( 64) hydrogen bonds : angle 4.81992 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 685 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 685 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 ILE cc_start: 0.8344 (mt) cc_final: 0.7534 (mm) REVERT: F 124 GLN cc_start: 0.7135 (tp-100) cc_final: 0.6931 (tm-30) REVERT: F 125 ILE cc_start: 0.8434 (mm) cc_final: 0.8199 (mm) REVERT: F 137 LEU cc_start: 0.8507 (mt) cc_final: 0.7735 (mt) REVERT: F 161 LEU cc_start: 0.6954 (pp) cc_final: 0.6611 (pp) REVERT: G 124 GLN cc_start: 0.7349 (tp40) cc_final: 0.6911 (tp-100) REVERT: G 145 ASP cc_start: 0.8063 (m-30) cc_final: 0.7842 (t0) REVERT: K 137 LEU cc_start: 0.8537 (mt) cc_final: 0.7481 (mt) REVERT: L 121 GLN cc_start: 0.8161 (tp40) cc_final: 0.7787 (tp40) REVERT: N 215 GLU cc_start: 0.5702 (tp30) cc_final: 0.5044 (tp30) outliers start: 0 outliers final: 0 residues processed: 685 average time/residue: 0.3698 time to fit residues: 373.1381 Evaluate side-chains 560 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 105 optimal weight: 0.0470 chunk 192 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 overall best weight: 2.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN C 85 ASN E 162 ASN G 85 ASN H 85 ASN K 104 ASN O 124 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.194605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.157876 restraints weight = 162050.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.162355 restraints weight = 118483.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.165821 restraints weight = 93966.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.168622 restraints weight = 78454.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.170617 restraints weight = 67494.573| |-----------------------------------------------------------------------------| r_work (final): 0.4602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 1.0118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21312 Z= 0.160 Angle : 0.547 4.879 28960 Z= 0.283 Chirality : 0.042 0.197 3024 Planarity : 0.005 0.055 3680 Dihedral : 4.478 14.503 2784 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.65 % Allowed : 12.38 % Favored : 86.98 % Rotamer: Outliers : 0.04 % Allowed : 1.53 % Favored : 98.43 % 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 aren not related in a simple way. whole: -4.06 (0.15), residues: 2480 helix: None (None), residues: 0 sheet: -2.90 (0.21), residues: 416 loop : -2.94 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 209 TYR 0.016 0.001 TYR P 65 PHE 0.011 0.001 PHE G 71 TRP 0.016 0.002 TRP F 122 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00346 (21296) covalent geometry : angle 0.54686 (28928) SS BOND : bond 0.00413 ( 16) SS BOND : angle 0.89870 ( 32) hydrogen bonds : bond 0.01013 ( 64) hydrogen bonds : angle 4.47144 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 697 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 696 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.7735 (tmm) cc_final: 0.7455 (tmm) REVERT: D 215 GLU cc_start: 0.5543 (mm-30) cc_final: 0.4709 (mp0) REVERT: F 215 GLU cc_start: 0.4899 (mm-30) cc_final: 0.4604 (mm-30) REVERT: G 124 GLN cc_start: 0.7386 (tp40) cc_final: 0.7037 (tm-30) REVERT: G 137 LEU cc_start: 0.8625 (mt) cc_final: 0.8044 (mt) REVERT: I 167 LYS cc_start: 0.7935 (mttp) cc_final: 0.7666 (mttp) REVERT: J 147 TRP cc_start: 0.7356 (p-90) cc_final: 0.6446 (p-90) REVERT: N 215 GLU cc_start: 0.5824 (tp30) cc_final: 0.5359 (tp30) outliers start: 1 outliers final: 0 residues processed: 696 average time/residue: 0.3751 time to fit residues: 387.1268 Evaluate side-chains 586 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 48 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 ASN J 162 ASN K 104 ASN ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN P 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.181208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.148131 restraints weight = 158324.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.151785 restraints weight = 116376.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.154605 restraints weight = 93101.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.156860 restraints weight = 77715.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.158478 restraints weight = 67404.078| |-----------------------------------------------------------------------------| r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 1.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21312 Z= 0.229 Angle : 0.685 8.520 28960 Z= 0.361 Chirality : 0.046 0.272 3024 Planarity : 0.007 0.077 3680 Dihedral : 5.648 26.367 2784 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.65 % Allowed : 16.49 % Favored : 82.86 % Rotamer: Outliers : 0.17 % Allowed : 2.49 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.29 (0.14), residues: 2480 helix: None (None), residues: 0 sheet: -3.12 (0.21), residues: 496 loop : -3.04 (0.12), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 209 TYR 0.030 0.002 TYR D 65 PHE 0.024 0.002 PHE D 198 TRP 0.026 0.002 TRP L 147 HIS 0.017 0.003 HIS L 207 Details of bonding type rmsd covalent geometry : bond 0.00480 (21296) covalent geometry : angle 0.68391 (28928) SS BOND : bond 0.00491 ( 16) SS BOND : angle 1.39114 ( 32) hydrogen bonds : bond 0.01703 ( 64) hydrogen bonds : angle 5.34002 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 720 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 716 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8639 (ttpt) REVERT: E 149 THR cc_start: 0.8591 (p) cc_final: 0.8389 (p) REVERT: F 67 LYS cc_start: 0.8053 (mttt) cc_final: 0.7842 (mmtt) REVERT: F 124 GLN cc_start: 0.7746 (tp-100) cc_final: 0.7381 (tm-30) REVERT: F 218 GLU cc_start: 0.6839 (pt0) cc_final: 0.6449 (pt0) REVERT: G 124 GLN cc_start: 0.7372 (tp40) cc_final: 0.7172 (tp-100) REVERT: G 125 ILE cc_start: 0.8859 (mm) cc_final: 0.7900 (mm) REVERT: G 137 LEU cc_start: 0.8759 (mt) cc_final: 0.8515 (mm) REVERT: G 167 LYS cc_start: 0.7280 (mptt) cc_final: 0.7054 (mptt) REVERT: J 147 TRP cc_start: 0.8186 (p-90) cc_final: 0.7198 (p-90) REVERT: J 162 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7602 (p0) REVERT: L 67 LYS cc_start: 0.8804 (tttt) cc_final: 0.8489 (tttt) REVERT: N 162 ASN cc_start: 0.7506 (p0) cc_final: 0.7163 (p0) REVERT: N 215 GLU cc_start: 0.5590 (tp30) cc_final: 0.5076 (tp30) REVERT: P 67 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8319 (ttpt) outliers start: 4 outliers final: 0 residues processed: 716 average time/residue: 0.4050 time to fit residues: 425.1898 Evaluate side-chains 572 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 571 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 37 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 205 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 225 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN I 104 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 ASN ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 ASN ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 85 ASN ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 85 ASN ** P 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.178306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.142779 restraints weight = 169760.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.147022 restraints weight = 120263.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.150347 restraints weight = 94145.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.152996 restraints weight = 77916.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.154848 restraints weight = 66847.632| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 1.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21312 Z= 0.174 Angle : 0.575 5.196 28960 Z= 0.299 Chirality : 0.042 0.146 3024 Planarity : 0.006 0.064 3680 Dihedral : 5.198 18.277 2784 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.65 % Allowed : 14.35 % Favored : 85.00 % Rotamer: Outliers : 0.04 % Allowed : 1.27 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.31 (0.14), residues: 2480 helix: None (None), residues: 0 sheet: -2.91 (0.21), residues: 544 loop : -3.12 (0.12), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 209 TYR 0.015 0.001 TYR P 65 PHE 0.010 0.001 PHE N 116 TRP 0.021 0.002 TRP J 147 HIS 0.004 0.001 HIS O 207 Details of bonding type rmsd covalent geometry : bond 0.00374 (21296) covalent geometry : angle 0.57364 (28928) SS BOND : bond 0.00401 ( 16) SS BOND : angle 1.24835 ( 32) hydrogen bonds : bond 0.01573 ( 64) hydrogen bonds : angle 5.34426 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 707 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 706 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8092 (mm110) REVERT: B 209 ARG cc_start: 0.9294 (mtm-85) cc_final: 0.9018 (mtm110) REVERT: C 214 MET cc_start: 0.7802 (tmm) cc_final: 0.7566 (tmm) REVERT: D 118 ASP cc_start: 0.8269 (t70) cc_final: 0.8037 (t70) REVERT: F 124 GLN cc_start: 0.7875 (tp-100) cc_final: 0.7324 (tm-30) REVERT: G 124 GLN cc_start: 0.7841 (tp40) cc_final: 0.7563 (tp-100) REVERT: G 125 ILE cc_start: 0.8713 (mm) cc_final: 0.7776 (mm) REVERT: I 81 ILE cc_start: 0.7576 (mm) cc_final: 0.7104 (tt) REVERT: K 81 ILE cc_start: 0.7431 (mt) cc_final: 0.7187 (tt) REVERT: L 81 ILE cc_start: 0.7892 (mt) cc_final: 0.7629 (tt) REVERT: M 167 LYS cc_start: 0.7422 (mtmt) cc_final: 0.7187 (mttp) REVERT: N 215 GLU cc_start: 0.6486 (tp30) cc_final: 0.5952 (tp30) REVERT: P 67 LYS cc_start: 0.8769 (ttpt) cc_final: 0.8341 (ttpt) outliers start: 1 outliers final: 0 residues processed: 706 average time/residue: 0.4007 time to fit residues: 418.1785 Evaluate side-chains 578 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 578 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 64 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN G 162 ASN I 66 HIS I 85 ASN I 104 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 ASN ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 85 ASN M 104 ASN ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN N 162 ASN ** O 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 104 ASN ** P 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.176088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.140964 restraints weight = 173018.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.145191 restraints weight = 122942.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.148490 restraints weight = 95886.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.151049 restraints weight = 79537.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.152857 restraints weight = 68247.560| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 1.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21312 Z= 0.185 Angle : 0.592 5.069 28960 Z= 0.311 Chirality : 0.042 0.145 3024 Planarity : 0.006 0.080 3680 Dihedral : 5.380 25.093 2784 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.60 % Allowed : 16.45 % Favored : 82.94 % Rotamer: Outliers : 0.09 % Allowed : 0.87 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.30 (0.14), residues: 2480 helix: None (None), residues: 0 sheet: -2.27 (0.24), residues: 464 loop : -3.32 (0.11), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 197 TYR 0.015 0.001 TYR I 65 PHE 0.015 0.002 PHE M 116 TRP 0.023 0.002 TRP H 163 HIS 0.006 0.001 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00395 (21296) covalent geometry : angle 0.59086 (28928) SS BOND : bond 0.00488 ( 16) SS BOND : angle 1.29859 ( 32) hydrogen bonds : bond 0.02191 ( 64) hydrogen bonds : angle 5.34244 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 700 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 698 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 ILE cc_start: 0.8813 (mt) cc_final: 0.8450 (pt) REVERT: B 209 ARG cc_start: 0.9349 (mtm-85) cc_final: 0.9059 (mtm110) REVERT: D 67 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8613 (ttpt) REVERT: D 118 ASP cc_start: 0.8325 (t70) cc_final: 0.8037 (t70) REVERT: F 82 THR cc_start: 0.6167 (m) cc_final: 0.5866 (m) REVERT: F 124 GLN cc_start: 0.8326 (tp-100) cc_final: 0.7771 (tm-30) REVERT: G 124 GLN cc_start: 0.8339 (tp40) cc_final: 0.7895 (tp40) REVERT: G 130 ILE cc_start: 0.8635 (mt) cc_final: 0.8221 (pt) REVERT: H 209 ARG cc_start: 0.8760 (mtm110) cc_final: 0.8518 (mtp-110) REVERT: I 81 ILE cc_start: 0.7852 (mm) cc_final: 0.7420 (tt) REVERT: J 82 THR cc_start: 0.6392 (p) cc_final: 0.6061 (m) REVERT: K 81 ILE cc_start: 0.7917 (mt) cc_final: 0.7665 (tt) REVERT: L 81 ILE cc_start: 0.8390 (mt) cc_final: 0.8177 (tt) REVERT: N 81 ILE cc_start: 0.8004 (mm) cc_final: 0.7751 (tt) REVERT: N 167 LYS cc_start: 0.7184 (mptt) cc_final: 0.6908 (mptt) REVERT: N 215 GLU cc_start: 0.6940 (tp30) cc_final: 0.6264 (tp30) REVERT: P 67 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8313 (ttpt) outliers start: 2 outliers final: 0 residues processed: 698 average time/residue: 0.3857 time to fit residues: 400.8693 Evaluate side-chains 576 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 198 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 170 optimal weight: 0.3980 chunk 202 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN F 104 ASN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN G 162 ASN H 104 ASN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 HIS J 104 ASN ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN ** N 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 HIS P 104 ASN ** P 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.170252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.135527 restraints weight = 172183.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.139691 restraints weight = 120826.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.142820 restraints weight = 93347.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.145353 restraints weight = 77063.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.147050 restraints weight = 65956.183| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 1.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21312 Z= 0.203 Angle : 0.619 5.518 28960 Z= 0.325 Chirality : 0.043 0.152 3024 Planarity : 0.007 0.091 3680 Dihedral : 5.586 21.244 2784 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.56 % Allowed : 16.73 % Favored : 82.70 % Rotamer: Outliers : 0.04 % Allowed : 0.74 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.37 (0.14), residues: 2480 helix: None (None), residues: 0 sheet: -3.02 (0.19), residues: 656 loop : -3.08 (0.12), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 209 TYR 0.016 0.002 TYR I 65 PHE 0.020 0.002 PHE M 108 TRP 0.026 0.002 TRP J 147 HIS 0.005 0.001 HIS N 207 Details of bonding type rmsd covalent geometry : bond 0.00435 (21296) covalent geometry : angle 0.61779 (28928) SS BOND : bond 0.00269 ( 16) SS BOND : angle 1.28822 ( 32) hydrogen bonds : bond 0.01968 ( 64) hydrogen bonds : angle 5.65648 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 689 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 688 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7992 (mttt) cc_final: 0.7785 (pttt) REVERT: B 130 ILE cc_start: 0.8901 (mt) cc_final: 0.8676 (pt) REVERT: B 209 ARG cc_start: 0.9354 (mtm-85) cc_final: 0.9039 (mtm110) REVERT: D 67 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8534 (ttpt) REVERT: E 81 ILE cc_start: 0.7449 (mt) cc_final: 0.7246 (tt) REVERT: E 116 PHE cc_start: 0.8557 (t80) cc_final: 0.8324 (t80) REVERT: F 124 GLN cc_start: 0.8441 (tp-100) cc_final: 0.8112 (tm-30) REVERT: F 125 ILE cc_start: 0.8925 (pt) cc_final: 0.8123 (pt) REVERT: F 144 ILE cc_start: 0.8862 (pt) cc_final: 0.8593 (pt) REVERT: G 124 GLN cc_start: 0.8342 (tp40) cc_final: 0.7878 (tp40) REVERT: G 155 TYR cc_start: 0.9025 (p90) cc_final: 0.8697 (p90) REVERT: H 116 PHE cc_start: 0.8634 (t80) cc_final: 0.8261 (t80) REVERT: H 209 ARG cc_start: 0.8929 (mtm110) cc_final: 0.8477 (mtp-110) REVERT: I 67 LYS cc_start: 0.8766 (tttt) cc_final: 0.8411 (tmmt) REVERT: I 81 ILE cc_start: 0.8259 (mm) cc_final: 0.7980 (tt) REVERT: L 67 LYS cc_start: 0.8821 (tttt) cc_final: 0.8507 (tttt) REVERT: M 67 LYS cc_start: 0.8475 (tttm) cc_final: 0.7862 (tttm) REVERT: M 218 GLU cc_start: 0.7325 (pt0) cc_final: 0.6786 (pt0) REVERT: N 139 GLN cc_start: 0.7540 (mt0) cc_final: 0.7287 (mt0) REVERT: N 143 ASP cc_start: 0.8812 (m-30) cc_final: 0.8399 (m-30) REVERT: N 215 GLU cc_start: 0.7084 (tp30) cc_final: 0.6365 (tp30) REVERT: O 67 LYS cc_start: 0.8585 (tttt) cc_final: 0.8261 (ttpt) REVERT: O 116 PHE cc_start: 0.8667 (t80) cc_final: 0.8409 (t80) REVERT: O 132 VAL cc_start: 0.9183 (t) cc_final: 0.8963 (t) REVERT: P 67 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8373 (ttpt) outliers start: 1 outliers final: 0 residues processed: 688 average time/residue: 0.4009 time to fit residues: 407.0876 Evaluate side-chains 571 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 82 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 208 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 69 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN G 162 ASN I 104 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.175427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.140488 restraints weight = 168953.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.144705 restraints weight = 118479.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.147965 restraints weight = 92095.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.150502 restraints weight = 75947.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.152366 restraints weight = 64985.282| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 1.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21312 Z= 0.113 Angle : 0.546 8.265 28960 Z= 0.278 Chirality : 0.043 0.160 3024 Planarity : 0.006 0.066 3680 Dihedral : 4.945 17.257 2784 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.70 % Favored : 86.81 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % 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 aren not related in a simple way. whole: -4.21 (0.14), residues: 2480 helix: None (None), residues: 0 sheet: -2.65 (0.20), residues: 592 loop : -3.11 (0.12), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 209 TYR 0.013 0.001 TYR F 177 PHE 0.013 0.001 PHE G 176 TRP 0.018 0.001 TRP E 163 HIS 0.002 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00256 (21296) covalent geometry : angle 0.54475 (28928) SS BOND : bond 0.00090 ( 16) SS BOND : angle 1.21230 ( 32) hydrogen bonds : bond 0.02167 ( 64) hydrogen bonds : angle 5.24211 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Evaluate side-chains 733 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 731 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 ILE cc_start: 0.8895 (mt) cc_final: 0.8658 (pt) REVERT: B 144 ILE cc_start: 0.8619 (pt) cc_final: 0.8276 (pt) REVERT: B 209 ARG cc_start: 0.9341 (mtm-85) cc_final: 0.9073 (mtm110) REVERT: C 81 ILE cc_start: 0.7747 (mm) cc_final: 0.7436 (tt) REVERT: C 116 PHE cc_start: 0.8805 (t80) cc_final: 0.8537 (t80) REVERT: C 130 ILE cc_start: 0.8691 (mt) cc_final: 0.8470 (mt) REVERT: C 167 LYS cc_start: 0.6324 (mptt) cc_final: 0.5943 (mptt) REVERT: C 214 MET cc_start: 0.7943 (tmm) cc_final: 0.7350 (tmm) REVERT: D 67 LYS cc_start: 0.8992 (ttmt) cc_final: 0.8609 (ttpt) REVERT: F 124 GLN cc_start: 0.8355 (tp-100) cc_final: 0.8109 (tm-30) REVERT: F 144 ILE cc_start: 0.8827 (pt) cc_final: 0.8607 (pt) REVERT: G 124 GLN cc_start: 0.8302 (tp40) cc_final: 0.7745 (tp-100) REVERT: G 155 TYR cc_start: 0.8931 (p90) cc_final: 0.8668 (p90) REVERT: H 116 PHE cc_start: 0.8607 (t80) cc_final: 0.8301 (t80) REVERT: H 209 ARG cc_start: 0.8855 (mtm110) cc_final: 0.8563 (mtp-110) REVERT: I 67 LYS cc_start: 0.8671 (tttt) cc_final: 0.8283 (tmmt) REVERT: I 81 ILE cc_start: 0.8094 (mm) cc_final: 0.7812 (tt) REVERT: L 67 LYS cc_start: 0.8868 (tttt) cc_final: 0.8545 (tttt) REVERT: L 150 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8634 (mmtt) REVERT: M 115 LYS cc_start: 0.7892 (mttt) cc_final: 0.7117 (pttm) REVERT: M 150 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8260 (mmtt) REVERT: N 139 GLN cc_start: 0.7620 (mt0) cc_final: 0.7404 (mt0) REVERT: N 167 LYS cc_start: 0.6827 (mptt) cc_final: 0.6495 (mptt) REVERT: N 215 GLU cc_start: 0.6606 (tp30) cc_final: 0.6075 (tp30) REVERT: O 67 LYS cc_start: 0.8425 (tttt) cc_final: 0.7850 (ttpt) REVERT: P 132 VAL cc_start: 0.9091 (t) cc_final: 0.8887 (t) REVERT: P 167 LYS cc_start: 0.7804 (mttp) cc_final: 0.7369 (mttp) outliers start: 2 outliers final: 0 residues processed: 731 average time/residue: 0.3924 time to fit residues: 427.2459 Evaluate side-chains 581 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 581 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 168 optimal weight: 0.4980 chunk 175 optimal weight: 4.9990 chunk 52 optimal weight: 0.0980 chunk 164 optimal weight: 0.1980 chunk 194 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 182 optimal weight: 10.0000 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN G 162 ASN I 104 ASN ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN L 104 ASN ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.177436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.141427 restraints weight = 167442.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.145879 restraints weight = 118040.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.148991 restraints weight = 91478.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.151523 restraints weight = 76141.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.153464 restraints weight = 65591.926| |-----------------------------------------------------------------------------| r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 1.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21312 Z= 0.098 Angle : 0.526 7.230 28960 Z= 0.267 Chirality : 0.043 0.153 3024 Planarity : 0.006 0.069 3680 Dihedral : 4.585 16.347 2784 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.73 % Favored : 88.83 % Rotamer: Outliers : 0.09 % Allowed : 0.13 % Favored : 99.78 % 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 aren not related in a simple way. whole: -4.07 (0.14), residues: 2480 helix: None (None), residues: 0 sheet: -2.40 (0.21), residues: 544 loop : -3.06 (0.12), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 209 TYR 0.010 0.001 TYR I 65 PHE 0.006 0.001 PHE I 71 TRP 0.014 0.001 TRP E 163 HIS 0.002 0.000 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00230 (21296) covalent geometry : angle 0.52522 (28928) SS BOND : bond 0.00073 ( 16) SS BOND : angle 1.04333 ( 32) hydrogen bonds : bond 0.02460 ( 64) hydrogen bonds : angle 4.96192 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8443.95 seconds wall clock time: 144 minutes 43.20 seconds (8683.20 seconds total)