Starting phenix.real_space_refine on Sat Oct 11 22:20:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qko_18468/10_2025/8qko_18468_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qko_18468/10_2025/8qko_18468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qko_18468/10_2025/8qko_18468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qko_18468/10_2025/8qko_18468.map" model { file = "/net/cci-nas-00/data/ceres_data/8qko_18468/10_2025/8qko_18468_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qko_18468/10_2025/8qko_18468_neut.cif" } resolution = 3.73 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 12396 2.51 5 N 2892 2.21 5 O 3108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18492 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "B" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "D" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "E" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "F" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "G" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "H" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "I" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "J" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "K" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "L" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Time building chain proxies: 4.92, per 1000 atoms: 0.27 Number of scatterers: 18492 At special positions: 0 Unit cell: (100.876, 98.2724, 158.798, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3108 8.00 N 2892 7.00 C 12396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 75.1% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 20 through 44 removed outlier: 3.993A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 69 Processing helix chain 'A' and resid 72 through 104 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 152 through 177 Processing helix chain 'A' and resid 202 through 235 Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 69 Processing helix chain 'B' and resid 72 through 104 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 152 through 177 Processing helix chain 'B' and resid 202 through 235 Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'C' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER C 42 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 69 Processing helix chain 'C' and resid 72 through 104 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 152 through 177 Processing helix chain 'C' and resid 202 through 235 Processing helix chain 'D' and resid 2 through 15 Processing helix chain 'D' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 69 Processing helix chain 'D' and resid 72 through 104 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 152 through 177 Processing helix chain 'D' and resid 202 through 235 Processing helix chain 'E' and resid 2 through 15 Processing helix chain 'E' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER E 42 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 69 Processing helix chain 'E' and resid 72 through 104 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 152 through 177 Processing helix chain 'E' and resid 202 through 235 Processing helix chain 'F' and resid 2 through 15 Processing helix chain 'F' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU F 41 " --> pdb=" O GLY F 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER F 42 " --> pdb=" O THR F 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 69 Processing helix chain 'F' and resid 72 through 104 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 152 through 177 Processing helix chain 'F' and resid 202 through 235 Processing helix chain 'G' and resid 2 through 15 Processing helix chain 'G' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 69 Processing helix chain 'G' and resid 72 through 104 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 152 through 177 Processing helix chain 'G' and resid 202 through 235 Processing helix chain 'H' and resid 2 through 15 Processing helix chain 'H' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU H 41 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 69 Processing helix chain 'H' and resid 72 through 104 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 152 through 177 Processing helix chain 'H' and resid 202 through 235 Processing helix chain 'I' and resid 2 through 15 Processing helix chain 'I' and resid 20 through 44 removed outlier: 3.995A pdb=" N VAL I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU I 41 " --> pdb=" O GLY I 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER I 42 " --> pdb=" O THR I 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 69 Processing helix chain 'I' and resid 72 through 104 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 152 through 177 Processing helix chain 'I' and resid 202 through 235 Processing helix chain 'J' and resid 2 through 15 Processing helix chain 'J' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU J 41 " --> pdb=" O GLY J 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER J 42 " --> pdb=" O THR J 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 69 Processing helix chain 'J' and resid 72 through 104 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 152 through 177 Processing helix chain 'J' and resid 202 through 235 Processing helix chain 'K' and resid 2 through 15 Processing helix chain 'K' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER K 42 " --> pdb=" O THR K 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA K 43 " --> pdb=" O ALA K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 69 Processing helix chain 'K' and resid 72 through 104 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 152 through 177 Processing helix chain 'K' and resid 202 through 235 Processing helix chain 'L' and resid 2 through 15 Processing helix chain 'L' and resid 20 through 44 removed outlier: 3.994A pdb=" N VAL L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER L 42 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 69 Processing helix chain 'L' and resid 72 through 104 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 152 through 177 Processing helix chain 'L' and resid 202 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.820A pdb=" N ARG A 52 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.820A pdb=" N ARG B 52 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.818A pdb=" N ARG C 52 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.818A pdb=" N ARG D 52 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.818A pdb=" N ARG E 52 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.819A pdb=" N ARG F 52 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.819A pdb=" N ARG G 52 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 removed outlier: 3.818A pdb=" N ARG H 52 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 removed outlier: 3.819A pdb=" N ARG I 52 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 removed outlier: 3.818A pdb=" N ARG J 52 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 removed outlier: 3.818A pdb=" N ARG K 52 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.818A pdb=" N ARG L 52 " --> pdb=" O PHE L 199 " (cutoff:3.500A) 1392 hydrogen bonds defined for protein. 4176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5412 1.34 - 1.46: 5116 1.46 - 1.58: 8360 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 19008 Sorted by residual: bond pdb=" CA VAL B 86 " pdb=" C VAL B 86 " ideal model delta sigma weight residual 1.523 1.533 -0.010 9.20e-03 1.18e+04 1.18e+00 bond pdb=" CA VAL D 86 " pdb=" C VAL D 86 " ideal model delta sigma weight residual 1.523 1.533 -0.010 9.20e-03 1.18e+04 1.16e+00 bond pdb=" CA VAL H 86 " pdb=" C VAL H 86 " ideal model delta sigma weight residual 1.523 1.533 -0.010 9.20e-03 1.18e+04 1.16e+00 bond pdb=" CA VAL L 86 " pdb=" C VAL L 86 " ideal model delta sigma weight residual 1.523 1.533 -0.010 9.20e-03 1.18e+04 1.16e+00 bond pdb=" CA VAL J 86 " pdb=" C VAL J 86 " ideal model delta sigma weight residual 1.523 1.533 -0.010 9.20e-03 1.18e+04 1.16e+00 ... (remaining 19003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 24937 1.10 - 2.21: 612 2.21 - 3.31: 131 3.31 - 4.42: 72 4.42 - 5.52: 48 Bond angle restraints: 25800 Sorted by residual: angle pdb=" C HIS G 194 " pdb=" CA HIS G 194 " pdb=" CB HIS G 194 " ideal model delta sigma weight residual 116.34 110.82 5.52 1.40e+00 5.10e-01 1.56e+01 angle pdb=" C HIS A 194 " pdb=" CA HIS A 194 " pdb=" CB HIS A 194 " ideal model delta sigma weight residual 116.34 110.82 5.52 1.40e+00 5.10e-01 1.56e+01 angle pdb=" C HIS I 194 " pdb=" CA HIS I 194 " pdb=" CB HIS I 194 " ideal model delta sigma weight residual 116.34 110.82 5.52 1.40e+00 5.10e-01 1.56e+01 angle pdb=" C HIS C 194 " pdb=" CA HIS C 194 " pdb=" CB HIS C 194 " ideal model delta sigma weight residual 116.34 110.82 5.52 1.40e+00 5.10e-01 1.56e+01 angle pdb=" C HIS F 194 " pdb=" CA HIS F 194 " pdb=" CB HIS F 194 " ideal model delta sigma weight residual 116.34 110.82 5.52 1.40e+00 5.10e-01 1.56e+01 ... (remaining 25795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.14: 9588 12.14 - 24.28: 876 24.28 - 36.43: 384 36.43 - 48.57: 168 48.57 - 60.71: 48 Dihedral angle restraints: 11064 sinusoidal: 4392 harmonic: 6672 Sorted by residual: dihedral pdb=" N ARG L 52 " pdb=" CA ARG L 52 " pdb=" CB ARG L 52 " pdb=" CG ARG L 52 " ideal model delta sinusoidal sigma weight residual 60.00 4.37 55.63 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" N ARG J 52 " pdb=" CA ARG J 52 " pdb=" CB ARG J 52 " pdb=" CG ARG J 52 " ideal model delta sinusoidal sigma weight residual 60.00 4.37 55.63 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" N ARG D 52 " pdb=" CA ARG D 52 " pdb=" CB ARG D 52 " pdb=" CG ARG D 52 " ideal model delta sinusoidal sigma weight residual 60.00 4.37 55.63 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 11061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1961 0.026 - 0.052: 588 0.052 - 0.079: 319 0.079 - 0.105: 72 0.105 - 0.131: 12 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA PRO F 203 " pdb=" N PRO F 203 " pdb=" C PRO F 203 " pdb=" CB PRO F 203 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA PRO A 203 " pdb=" N PRO A 203 " pdb=" C PRO A 203 " pdb=" CB PRO A 203 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA PRO E 203 " pdb=" N PRO E 203 " pdb=" C PRO E 203 " pdb=" CB PRO E 203 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 2949 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 52 " -0.159 9.50e-02 1.11e+02 7.14e-02 3.15e+00 pdb=" NE ARG E 52 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG E 52 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG E 52 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 52 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 52 " -0.159 9.50e-02 1.11e+02 7.11e-02 3.14e+00 pdb=" NE ARG F 52 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG F 52 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG F 52 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG F 52 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 52 " 0.158 9.50e-02 1.11e+02 7.10e-02 3.13e+00 pdb=" NE ARG I 52 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG I 52 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG I 52 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG I 52 " 0.007 2.00e-02 2.50e+03 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 89 2.37 - 3.00: 10689 3.00 - 3.63: 30943 3.63 - 4.27: 40588 4.27 - 4.90: 68823 Nonbonded interactions: 151132 Sorted by model distance: nonbonded pdb=" OG1 THR B 204 " pdb=" OD1 ASP C 66 " model vdw 1.736 3.040 nonbonded pdb=" OD1 ASP A 66 " pdb=" OG1 THR K 204 " model vdw 1.804 3.040 nonbonded pdb=" ND2 ASN A 62 " pdb=" O LEU K 200 " model vdw 1.965 3.120 nonbonded pdb=" N ASN B 62 " pdb=" NH2 ARG H 52 " model vdw 2.195 3.200 nonbonded pdb=" NH2 ARG B 100 " pdb=" OD2 ASP H 11 " model vdw 2.201 3.120 ... (remaining 151127 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: 0.07 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' } 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: 5.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 19.240 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 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 : 0.003 0.031 19044 Z= 0.147 Angle : 0.523 5.523 25872 Z= 0.279 Chirality : 0.034 0.131 2952 Planarity : 0.006 0.071 3096 Dihedral : 13.371 60.712 6636 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.14 % Allowed : 2.94 % Favored : 93.92 % 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: 2.37 (0.17), residues: 2220 helix: 2.83 (0.11), residues: 1632 sheet: -1.84 (0.30), residues: 204 loop : -2.26 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 52 TYR 0.005 0.001 TYR K 155 PHE 0.013 0.001 PHE G 31 TRP 0.006 0.001 TRP A 77 HIS 0.003 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00317 (19008) covalent geometry : angle 0.52212 (25800) SS BOND : bond 0.00247 ( 36) SS BOND : angle 0.65984 ( 72) hydrogen bonds : bond 0.11078 ( 1392) hydrogen bonds : angle 4.24420 ( 4176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 597 time to evaluate : 0.580 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: A 56 GLN cc_start: 0.9310 (mt0) cc_final: 0.8787 (mt0) REVERT: A 61 GLU cc_start: 0.8814 (mm-30) cc_final: 0.7960 (mm-30) REVERT: B 48 GLN cc_start: 0.9515 (OUTLIER) cc_final: 0.8940 (tp40) REVERT: B 56 GLN cc_start: 0.9247 (mt0) cc_final: 0.8550 (mp10) REVERT: B 61 GLU cc_start: 0.8765 (mm-30) cc_final: 0.7878 (mm-30) REVERT: B 65 TYR cc_start: 0.9215 (t80) cc_final: 0.8982 (t80) REVERT: B 227 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8737 (mm-30) REVERT: C 32 ARG cc_start: 0.9091 (ttm-80) cc_final: 0.8690 (ttm170) REVERT: C 46 ASP cc_start: 0.6950 (p0) cc_final: 0.6681 (p0) REVERT: C 76 PHE cc_start: 0.7676 (t80) cc_final: 0.7318 (t80) REVERT: C 164 ILE cc_start: 0.9268 (mm) cc_final: 0.8905 (pt) REVERT: C 210 ILE cc_start: 0.8713 (mt) cc_final: 0.8222 (mt) REVERT: D 22 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.6999 (tttm) REVERT: D 61 GLU cc_start: 0.7830 (mm-30) cc_final: 0.6588 (mm-30) REVERT: D 86 VAL cc_start: 0.8878 (t) cc_final: 0.8661 (t) REVERT: D 164 ILE cc_start: 0.8755 (mm) cc_final: 0.8359 (pt) REVERT: D 196 VAL cc_start: 0.5985 (p) cc_final: 0.5352 (t) REVERT: E 22 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6676 (ttmt) REVERT: E 61 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7377 (mm-30) REVERT: E 65 TYR cc_start: 0.8241 (t80) cc_final: 0.7501 (t80) REVERT: F 8 LYS cc_start: 0.9562 (pttp) cc_final: 0.9356 (ptpp) REVERT: F 65 TYR cc_start: 0.8697 (t80) cc_final: 0.8198 (t80) REVERT: F 162 LYS cc_start: 0.7626 (ttmm) cc_final: 0.6971 (mttm) REVERT: F 173 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8798 (tm-30) REVERT: F 197 ASP cc_start: 0.9033 (m-30) cc_final: 0.8511 (m-30) REVERT: F 205 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: F 227 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8038 (mm-30) REVERT: G 22 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7330 (pttm) REVERT: G 25 LEU cc_start: 0.9447 (mt) cc_final: 0.9211 (pp) REVERT: G 154 THR cc_start: 0.7582 (p) cc_final: 0.7042 (p) REVERT: G 199 PHE cc_start: 0.7316 (m-80) cc_final: 0.5948 (m-80) REVERT: G 213 MET cc_start: 0.7698 (mmp) cc_final: 0.6815 (mmp) REVERT: H 61 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6866 (mm-30) REVERT: H 88 THR cc_start: 0.7799 (p) cc_final: 0.7315 (p) REVERT: H 166 GLU cc_start: 0.9047 (tp30) cc_final: 0.8476 (tp30) REVERT: H 205 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: H 227 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7919 (mm-30) REVERT: I 71 ILE cc_start: 0.8601 (tp) cc_final: 0.7946 (tt) REVERT: I 206 LYS cc_start: 0.8422 (mttm) cc_final: 0.8112 (mptt) REVERT: J 71 ILE cc_start: 0.7836 (tp) cc_final: 0.7533 (tt) REVERT: J 217 SER cc_start: 0.9108 (m) cc_final: 0.8703 (p) REVERT: J 231 VAL cc_start: 0.9085 (t) cc_final: 0.8829 (t) REVERT: K 227 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8561 (mm-30) REVERT: L 80 GLN cc_start: 0.8550 (tt0) cc_final: 0.8256 (tm-30) REVERT: L 156 ILE cc_start: 0.9380 (mm) cc_final: 0.9058 (mm) REVERT: L 188 LYS cc_start: 0.8828 (mmmm) cc_final: 0.8416 (mptt) REVERT: L 218 LEU cc_start: 0.9445 (mm) cc_final: 0.9230 (mm) REVERT: L 225 ILE cc_start: 0.9538 (mm) cc_final: 0.9323 (pt) outliers start: 64 outliers final: 11 residues processed: 632 average time/residue: 0.1546 time to fit residues: 144.1336 Evaluate side-chains 363 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 346 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 22 LYS Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 52 ARG Chi-restraints excluded: chain H residue 205 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 57 GLN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 GLN D 80 GLN G 195 GLN H 14 GLN H 80 GLN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN J 73 HIS ** J 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN K 48 GLN K 56 GLN K 73 HIS K 195 GLN L 173 GLN L 195 GLN L 224 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.077178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.064169 restraints weight = 80217.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.065909 restraints weight = 40825.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067081 restraints weight = 25382.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.067929 restraints weight = 17921.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.068351 restraints weight = 13829.342| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 19044 Z= 0.149 Angle : 0.664 11.991 25872 Z= 0.326 Chirality : 0.040 0.300 2952 Planarity : 0.004 0.050 3096 Dihedral : 5.263 50.478 2483 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.48 % Allowed : 14.26 % Favored : 82.25 % 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: 2.27 (0.17), residues: 2220 helix: 2.58 (0.11), residues: 1668 sheet: -1.58 (0.32), residues: 204 loop : -2.04 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 202 TYR 0.018 0.001 TYR D 91 PHE 0.028 0.001 PHE G 165 TRP 0.027 0.001 TRP J 24 HIS 0.007 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00351 (19008) covalent geometry : angle 0.65844 (25800) SS BOND : bond 0.00561 ( 36) SS BOND : angle 1.73735 ( 72) hydrogen bonds : bond 0.03400 ( 1392) hydrogen bonds : angle 3.33334 ( 4176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 393 time to evaluate : 0.783 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: A 61 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8320 (mm-30) REVERT: A 91 TYR cc_start: 0.8580 (t80) cc_final: 0.8326 (t80) REVERT: B 48 GLN cc_start: 0.9543 (OUTLIER) cc_final: 0.9016 (tp40) REVERT: B 56 GLN cc_start: 0.9378 (mt0) cc_final: 0.8485 (mt0) REVERT: B 61 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7914 (mm-30) REVERT: B 65 TYR cc_start: 0.9168 (t80) cc_final: 0.8877 (t80) REVERT: B 91 TYR cc_start: 0.8422 (t80) cc_final: 0.8177 (t80) REVERT: C 164 ILE cc_start: 0.9330 (mm) cc_final: 0.9002 (pt) REVERT: D 41 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7637 (mt-10) REVERT: D 53 CYS cc_start: 0.4871 (OUTLIER) cc_final: 0.3612 (p) REVERT: D 164 ILE cc_start: 0.8883 (mm) cc_final: 0.8460 (pt) REVERT: E 56 GLN cc_start: 0.9398 (mt0) cc_final: 0.9045 (mt0) REVERT: F 52 ARG cc_start: 0.7430 (mtm-85) cc_final: 0.7024 (mtm-85) REVERT: F 173 GLN cc_start: 0.9346 (tm-30) cc_final: 0.8848 (tm-30) REVERT: F 227 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8172 (mm-30) REVERT: G 25 LEU cc_start: 0.9465 (mt) cc_final: 0.9184 (pp) REVERT: G 32 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8384 (ptp-110) REVERT: G 63 VAL cc_start: 0.9255 (m) cc_final: 0.8902 (p) REVERT: H 41 GLU cc_start: 0.8521 (tp30) cc_final: 0.8114 (tm-30) REVERT: H 99 MET cc_start: 0.8875 (mmp) cc_final: 0.8319 (mmp) REVERT: H 166 GLU cc_start: 0.9192 (tp30) cc_final: 0.8830 (tp30) REVERT: H 173 GLN cc_start: 0.8961 (tm-30) cc_final: 0.8684 (tm-30) REVERT: H 205 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7544 (mp0) REVERT: I 188 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8708 (mmmm) REVERT: J 75 ARG cc_start: 0.8699 (mpp80) cc_final: 0.8298 (mmt90) REVERT: J 212 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8626 (t80) REVERT: L 67 LYS cc_start: 0.8919 (tppt) cc_final: 0.8714 (ttmm) REVERT: L 80 GLN cc_start: 0.8772 (tt0) cc_final: 0.8250 (tt0) REVERT: L 188 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8592 (mptt) REVERT: L 218 LEU cc_start: 0.9562 (mm) cc_final: 0.9322 (mm) outliers start: 71 outliers final: 38 residues processed: 438 average time/residue: 0.1429 time to fit residues: 95.2714 Evaluate side-chains 362 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 320 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 32 ARG Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 213 MET Chi-restraints excluded: chain J residue 224 ASN Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 48 GLN Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 197 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN B 48 GLN B 54 ASN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN C 54 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN D 80 GLN F 48 GLN F 54 ASN G 54 ASN ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 ASN K 194 HIS L 73 HIS L 195 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.069563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.056915 restraints weight = 83498.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.058470 restraints weight = 40936.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.059613 restraints weight = 24918.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.060310 restraints weight = 17812.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.060848 restraints weight = 14096.218| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 19044 Z= 0.255 Angle : 0.723 11.530 25872 Z= 0.382 Chirality : 0.044 0.347 2952 Planarity : 0.005 0.074 3096 Dihedral : 5.156 59.740 2453 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.85 % Allowed : 17.84 % Favored : 77.30 % 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: 1.78 (0.17), residues: 2220 helix: 2.27 (0.11), residues: 1656 sheet: -1.92 (0.32), residues: 204 loop : -2.19 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 202 TYR 0.026 0.002 TYR E 91 PHE 0.034 0.002 PHE G 165 TRP 0.020 0.002 TRP J 44 HIS 0.011 0.002 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00557 (19008) covalent geometry : angle 0.71645 (25800) SS BOND : bond 0.02272 ( 36) SS BOND : angle 1.99257 ( 72) hydrogen bonds : bond 0.04143 ( 1392) hydrogen bonds : angle 3.60352 ( 4176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 310 time to evaluate : 0.810 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: A 46 ASP cc_start: 0.8583 (p0) cc_final: 0.7953 (p0) REVERT: A 61 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8117 (tp30) REVERT: A 91 TYR cc_start: 0.8724 (t80) cc_final: 0.8314 (t80) REVERT: B 46 ASP cc_start: 0.8598 (p0) cc_final: 0.8113 (p0) REVERT: B 56 GLN cc_start: 0.9411 (mt0) cc_final: 0.8943 (mt0) REVERT: C 38 THR cc_start: 0.8917 (t) cc_final: 0.8440 (t) REVERT: C 179 PHE cc_start: 0.8143 (m-80) cc_final: 0.7903 (m-80) REVERT: D 41 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8056 (tm-30) REVERT: D 154 THR cc_start: 0.8522 (p) cc_final: 0.8309 (t) REVERT: D 157 ILE cc_start: 0.8729 (mm) cc_final: 0.8510 (mm) REVERT: E 47 GLU cc_start: 0.8577 (tp30) cc_final: 0.8330 (tp30) REVERT: E 56 GLN cc_start: 0.9493 (mt0) cc_final: 0.9194 (mt0) REVERT: E 227 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8890 (mm-30) REVERT: F 26 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8514 (m) REVERT: F 48 GLN cc_start: 0.9537 (OUTLIER) cc_final: 0.9029 (tp40) REVERT: F 56 GLN cc_start: 0.9203 (pt0) cc_final: 0.8709 (pt0) REVERT: F 173 GLN cc_start: 0.9653 (tm-30) cc_final: 0.8984 (tm-30) REVERT: F 195 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.9019 (mp10) REVERT: F 205 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8554 (mt-10) REVERT: F 227 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8578 (mm-30) REVERT: G 56 GLN cc_start: 0.9437 (mm-40) cc_final: 0.9143 (mm-40) REVERT: G 63 VAL cc_start: 0.9395 (m) cc_final: 0.9115 (p) REVERT: G 165 PHE cc_start: 0.8322 (m-80) cc_final: 0.7916 (m-80) REVERT: H 8 LYS cc_start: 0.9634 (pttp) cc_final: 0.9364 (ptpp) REVERT: H 41 GLU cc_start: 0.8757 (tp30) cc_final: 0.8505 (tm-30) REVERT: H 61 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8507 (tp30) REVERT: H 166 GLU cc_start: 0.9342 (tp30) cc_final: 0.8979 (tp30) REVERT: H 173 GLN cc_start: 0.9371 (tm-30) cc_final: 0.9093 (tm-30) REVERT: J 47 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7580 (mp0) REVERT: J 52 ARG cc_start: 0.8770 (ptp90) cc_final: 0.8455 (mpp80) REVERT: J 56 GLN cc_start: 0.9127 (mt0) cc_final: 0.8631 (mt0) REVERT: J 75 ARG cc_start: 0.9322 (mpp80) cc_final: 0.8446 (mtt-85) REVERT: J 165 PHE cc_start: 0.8603 (m-10) cc_final: 0.8391 (m-10) REVERT: K 14 GLN cc_start: 0.8501 (pt0) cc_final: 0.7927 (pt0) REVERT: K 46 ASP cc_start: 0.8592 (p0) cc_final: 0.8358 (p0) REVERT: K 166 GLU cc_start: 0.8698 (tp30) cc_final: 0.8384 (tp30) REVERT: L 47 GLU cc_start: 0.8645 (pt0) cc_final: 0.8236 (pt0) REVERT: L 48 GLN cc_start: 0.8335 (pm20) cc_final: 0.7825 (tt0) REVERT: L 188 LYS cc_start: 0.9376 (mmmm) cc_final: 0.8962 (tppp) REVERT: L 197 ASP cc_start: 0.8227 (m-30) cc_final: 0.7984 (m-30) outliers start: 99 outliers final: 56 residues processed: 381 average time/residue: 0.1526 time to fit residues: 87.0571 Evaluate side-chains 322 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 263 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain D residue 16 TYR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 66 ASP Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 31 PHE Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 195 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 183 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 19 optimal weight: 40.0000 chunk 158 optimal weight: 0.1980 chunk 64 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN H 56 GLN H 195 GLN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.068745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.055785 restraints weight = 83062.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.057352 restraints weight = 39512.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.058476 restraints weight = 23952.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.059105 restraints weight = 17093.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.059704 restraints weight = 13787.832| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19044 Z= 0.141 Angle : 0.618 13.583 25872 Z= 0.305 Chirality : 0.038 0.230 2952 Planarity : 0.004 0.043 3096 Dihedral : 4.705 51.665 2448 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.31 % Allowed : 19.46 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.17), residues: 2220 helix: 2.61 (0.11), residues: 1668 sheet: -1.85 (0.33), residues: 204 loop : -2.13 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 52 TYR 0.019 0.001 TYR D 65 PHE 0.035 0.001 PHE G 165 TRP 0.013 0.001 TRP J 24 HIS 0.009 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00324 (19008) covalent geometry : angle 0.61550 (25800) SS BOND : bond 0.00373 ( 36) SS BOND : angle 1.24014 ( 72) hydrogen bonds : bond 0.03248 ( 1392) hydrogen bonds : angle 3.27043 ( 4176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 302 time to evaluate : 0.951 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: B 56 GLN cc_start: 0.9431 (mt0) cc_final: 0.8703 (mt0) REVERT: C 160 LEU cc_start: 0.9550 (tp) cc_final: 0.9242 (tt) REVERT: C 188 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8688 (mmmm) REVERT: D 47 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: D 56 GLN cc_start: 0.9424 (mt0) cc_final: 0.9130 (mt0) REVERT: D 61 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8389 (mm-30) REVERT: D 157 ILE cc_start: 0.8824 (mm) cc_final: 0.8621 (mm) REVERT: E 56 GLN cc_start: 0.9478 (mt0) cc_final: 0.9031 (mt0) REVERT: E 227 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8955 (mm-30) REVERT: F 26 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8739 (m) REVERT: F 52 ARG cc_start: 0.8043 (mtm110) cc_final: 0.7588 (mtm110) REVERT: F 56 GLN cc_start: 0.9176 (pt0) cc_final: 0.8665 (pt0) REVERT: F 173 GLN cc_start: 0.9620 (tm-30) cc_final: 0.8965 (tm-30) REVERT: F 195 GLN cc_start: 0.9138 (pm20) cc_final: 0.8817 (pt0) REVERT: F 205 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8618 (mt-10) REVERT: F 227 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8711 (mm-30) REVERT: G 22 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8339 (ptpp) REVERT: G 47 GLU cc_start: 0.8325 (pm20) cc_final: 0.8107 (pm20) REVERT: G 61 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7697 (tm-30) REVERT: G 63 VAL cc_start: 0.9457 (m) cc_final: 0.9190 (p) REVERT: G 83 PHE cc_start: 0.9340 (m-10) cc_final: 0.9083 (m-10) REVERT: G 165 PHE cc_start: 0.8528 (m-80) cc_final: 0.8081 (m-80) REVERT: G 188 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8806 (mmmm) REVERT: H 41 GLU cc_start: 0.8732 (tp30) cc_final: 0.8511 (tm-30) REVERT: H 65 TYR cc_start: 0.9320 (t80) cc_final: 0.9041 (t80) REVERT: H 166 GLU cc_start: 0.9346 (tp30) cc_final: 0.8987 (tp30) REVERT: H 173 GLN cc_start: 0.9320 (tm-30) cc_final: 0.9116 (tm-30) REVERT: H 195 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7465 (pp30) REVERT: I 52 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8081 (ptp90) REVERT: I 165 PHE cc_start: 0.8391 (m-80) cc_final: 0.7998 (m-80) REVERT: J 56 GLN cc_start: 0.9113 (mt0) cc_final: 0.8474 (mt0) REVERT: J 75 ARG cc_start: 0.9271 (mpp80) cc_final: 0.8386 (mtt-85) REVERT: K 14 GLN cc_start: 0.8430 (pt0) cc_final: 0.7911 (pt0) REVERT: K 83 PHE cc_start: 0.9449 (OUTLIER) cc_final: 0.9063 (t80) REVERT: K 205 GLU cc_start: 0.9191 (tp30) cc_final: 0.8968 (tp30) REVERT: L 14 GLN cc_start: 0.8936 (pt0) cc_final: 0.8561 (pt0) REVERT: L 47 GLU cc_start: 0.8617 (pt0) cc_final: 0.8409 (pm20) REVERT: L 67 LYS cc_start: 0.9191 (tppt) cc_final: 0.8725 (tptp) REVERT: L 166 GLU cc_start: 0.9427 (tp30) cc_final: 0.9151 (tp30) outliers start: 88 outliers final: 51 residues processed: 360 average time/residue: 0.1511 time to fit residues: 81.9404 Evaluate side-chains 333 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 276 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 52 ARG Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 31 PHE Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 83 PHE Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 173 GLN Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 93 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN F 224 ASN ** G 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN J 224 ASN ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.066252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.053471 restraints weight = 84623.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.054984 restraints weight = 39808.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.055974 restraints weight = 24357.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.056680 restraints weight = 17580.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.057163 restraints weight = 14096.686| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.7570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19044 Z= 0.202 Angle : 0.628 11.661 25872 Z= 0.319 Chirality : 0.039 0.332 2952 Planarity : 0.004 0.066 3096 Dihedral : 4.677 51.637 2448 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.71 % Allowed : 19.71 % Favored : 75.59 % 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: 2.28 (0.17), residues: 2220 helix: 2.64 (0.11), residues: 1668 sheet: -1.96 (0.33), residues: 204 loop : -2.12 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 189 TYR 0.023 0.001 TYR D 65 PHE 0.028 0.001 PHE G 165 TRP 0.011 0.001 TRP H 77 HIS 0.024 0.002 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00456 (19008) covalent geometry : angle 0.62540 (25800) SS BOND : bond 0.00345 ( 36) SS BOND : angle 1.30147 ( 72) hydrogen bonds : bond 0.03332 ( 1392) hydrogen bonds : angle 3.33949 ( 4176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 280 time to evaluate : 0.717 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: A 46 ASP cc_start: 0.8464 (p0) cc_final: 0.7887 (p0) REVERT: A 61 GLU cc_start: 0.8989 (tp30) cc_final: 0.8783 (mm-30) REVERT: B 56 GLN cc_start: 0.9444 (mt0) cc_final: 0.8707 (mt0) REVERT: C 160 LEU cc_start: 0.9618 (tp) cc_final: 0.9230 (pp) REVERT: D 41 GLU cc_start: 0.8133 (pm20) cc_final: 0.7910 (pm20) REVERT: D 56 GLN cc_start: 0.9479 (mt0) cc_final: 0.9254 (mt0) REVERT: D 154 THR cc_start: 0.8734 (p) cc_final: 0.8492 (t) REVERT: D 188 LYS cc_start: 0.9046 (mmmm) cc_final: 0.8600 (mmmm) REVERT: E 56 GLN cc_start: 0.9463 (mt0) cc_final: 0.9225 (mt0) REVERT: F 56 GLN cc_start: 0.9335 (pt0) cc_final: 0.8793 (pt0) REVERT: F 173 GLN cc_start: 0.9650 (tm-30) cc_final: 0.8942 (tm-30) REVERT: F 195 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8971 (mt0) REVERT: F 205 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8434 (mt-10) REVERT: F 227 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8787 (mm-30) REVERT: G 16 TYR cc_start: 0.6734 (OUTLIER) cc_final: 0.6517 (m-10) REVERT: G 47 GLU cc_start: 0.8321 (pm20) cc_final: 0.8116 (pm20) REVERT: G 188 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8803 (mmmm) REVERT: H 92 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9042 (tt) REVERT: H 166 GLU cc_start: 0.9342 (tp30) cc_final: 0.8973 (tp30) REVERT: H 173 GLN cc_start: 0.9406 (tm-30) cc_final: 0.9140 (tm-30) REVERT: I 47 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7921 (mm-30) REVERT: I 52 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8191 (ptp90) REVERT: I 165 PHE cc_start: 0.8632 (m-80) cc_final: 0.8274 (m-80) REVERT: J 56 GLN cc_start: 0.9238 (mt0) cc_final: 0.8618 (mt0) REVERT: K 83 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.9171 (t80) REVERT: K 166 GLU cc_start: 0.9263 (tp30) cc_final: 0.9034 (tp30) REVERT: L 14 GLN cc_start: 0.8887 (pt0) cc_final: 0.8550 (pt0) REVERT: L 67 LYS cc_start: 0.9202 (tppt) cc_final: 0.8933 (tptp) outliers start: 96 outliers final: 61 residues processed: 346 average time/residue: 0.1536 time to fit residues: 79.9408 Evaluate side-chains 326 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 260 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 16 TYR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain G residue 16 TYR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 52 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 31 PHE Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 83 PHE Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 173 GLN Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 20 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 163 optimal weight: 30.0000 chunk 57 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 80 optimal weight: 0.0970 chunk 109 optimal weight: 40.0000 chunk 199 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 HIS ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.065645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.053021 restraints weight = 83621.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.054464 restraints weight = 38827.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.055565 restraints weight = 23544.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.056111 restraints weight = 16802.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.056595 restraints weight = 13783.207| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.8207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19044 Z= 0.168 Angle : 0.625 13.212 25872 Z= 0.310 Chirality : 0.039 0.416 2952 Planarity : 0.004 0.038 3096 Dihedral : 4.500 57.574 2446 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.31 % Allowed : 21.42 % Favored : 74.26 % 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: 2.36 (0.18), residues: 2220 helix: 2.72 (0.11), residues: 1668 sheet: -1.96 (0.34), residues: 204 loop : -2.18 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 52 TYR 0.028 0.001 TYR F 65 PHE 0.024 0.001 PHE I 232 TRP 0.013 0.001 TRP J 24 HIS 0.006 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00387 (19008) covalent geometry : angle 0.62250 (25800) SS BOND : bond 0.00271 ( 36) SS BOND : angle 1.15462 ( 72) hydrogen bonds : bond 0.03170 ( 1392) hydrogen bonds : angle 3.27297 ( 4176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 283 time to evaluate : 0.814 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: A 52 ARG cc_start: 0.7711 (mpp-170) cc_final: 0.7251 (mtm-85) REVERT: A 91 TYR cc_start: 0.8700 (t80) cc_final: 0.8482 (t80) REVERT: B 56 GLN cc_start: 0.9435 (mt0) cc_final: 0.8661 (mt0) REVERT: B 61 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8445 (mm-30) REVERT: B 91 TYR cc_start: 0.8606 (t80) cc_final: 0.8317 (t80) REVERT: B 205 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8548 (mm-30) REVERT: C 56 GLN cc_start: 0.9621 (mt0) cc_final: 0.8962 (mt0) REVERT: C 160 LEU cc_start: 0.9651 (tp) cc_final: 0.9301 (pp) REVERT: D 41 GLU cc_start: 0.8148 (pm20) cc_final: 0.7937 (pm20) REVERT: D 47 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: D 48 GLN cc_start: 0.9533 (tp40) cc_final: 0.9138 (tp40) REVERT: D 56 GLN cc_start: 0.9478 (mt0) cc_final: 0.8627 (mp10) REVERT: D 188 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8815 (mmmm) REVERT: F 56 GLN cc_start: 0.9289 (pt0) cc_final: 0.9070 (pt0) REVERT: F 166 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8862 (tm-30) REVERT: F 173 GLN cc_start: 0.9640 (tm-30) cc_final: 0.8912 (tm-30) REVERT: F 195 GLN cc_start: 0.9228 (pm20) cc_final: 0.8943 (pt0) REVERT: F 205 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8665 (mt-10) REVERT: F 227 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8765 (mm-30) REVERT: G 188 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8683 (mmmm) REVERT: H 92 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9108 (tt) REVERT: H 166 GLU cc_start: 0.9352 (tp30) cc_final: 0.8977 (tp30) REVERT: H 173 GLN cc_start: 0.9405 (tm-30) cc_final: 0.9150 (tm-30) REVERT: H 195 GLN cc_start: 0.8441 (pp30) cc_final: 0.7729 (pp30) REVERT: I 47 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7833 (mm-30) REVERT: I 52 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8104 (ptp90) REVERT: K 91 TYR cc_start: 0.8916 (t80) cc_final: 0.8576 (t80) REVERT: L 14 GLN cc_start: 0.8840 (pt0) cc_final: 0.8525 (pt0) REVERT: L 89 LEU cc_start: 0.9683 (tp) cc_final: 0.9473 (tt) REVERT: L 166 GLU cc_start: 0.9443 (tp30) cc_final: 0.9190 (tp30) REVERT: L 188 LYS cc_start: 0.9436 (mmmm) cc_final: 0.8832 (tppp) outliers start: 88 outliers final: 66 residues processed: 349 average time/residue: 0.1552 time to fit residues: 80.7503 Evaluate side-chains 325 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 256 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 52 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 31 PHE Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 173 GLN Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 140 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN J 224 ASN K 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.065830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.053158 restraints weight = 83996.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.054658 restraints weight = 38100.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.055731 restraints weight = 22996.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.056370 restraints weight = 16296.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.056831 restraints weight = 13107.579| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.8456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19044 Z= 0.132 Angle : 0.621 14.812 25872 Z= 0.304 Chirality : 0.038 0.306 2952 Planarity : 0.004 0.038 3096 Dihedral : 4.398 49.110 2446 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.17 % Allowed : 22.60 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.18), residues: 2220 helix: 2.73 (0.12), residues: 1680 sheet: -1.95 (0.33), residues: 204 loop : -2.06 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 52 TYR 0.030 0.001 TYR H 65 PHE 0.020 0.001 PHE I 232 TRP 0.012 0.001 TRP J 24 HIS 0.010 0.001 HIS F 194 Details of bonding type rmsd covalent geometry : bond 0.00305 (19008) covalent geometry : angle 0.61997 (25800) SS BOND : bond 0.00262 ( 36) SS BOND : angle 1.01218 ( 72) hydrogen bonds : bond 0.03062 ( 1392) hydrogen bonds : angle 3.23423 ( 4176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 279 time to evaluate : 0.707 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: A 52 ARG cc_start: 0.7648 (mpp-170) cc_final: 0.7273 (mtm-85) REVERT: A 61 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8342 (mm-30) REVERT: A 91 TYR cc_start: 0.8759 (t80) cc_final: 0.8493 (t80) REVERT: B 56 GLN cc_start: 0.9410 (mt0) cc_final: 0.8617 (mt0) REVERT: B 91 TYR cc_start: 0.8655 (t80) cc_final: 0.8312 (t80) REVERT: B 195 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7926 (pp30) REVERT: B 205 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8530 (mm-30) REVERT: C 48 GLN cc_start: 0.9477 (tp40) cc_final: 0.9194 (tp40) REVERT: C 56 GLN cc_start: 0.9615 (mt0) cc_final: 0.8737 (mt0) REVERT: C 160 LEU cc_start: 0.9653 (tp) cc_final: 0.9331 (pp) REVERT: D 34 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9389 (pp) REVERT: D 48 GLN cc_start: 0.9512 (tp40) cc_final: 0.9173 (tp40) REVERT: D 56 GLN cc_start: 0.9480 (mt0) cc_final: 0.8486 (mt0) REVERT: D 188 LYS cc_start: 0.9163 (mmmm) cc_final: 0.8836 (mmmm) REVERT: E 56 GLN cc_start: 0.9449 (mt0) cc_final: 0.8317 (mt0) REVERT: F 52 ARG cc_start: 0.7869 (mtm110) cc_final: 0.6779 (mtm-85) REVERT: F 56 GLN cc_start: 0.9290 (pt0) cc_final: 0.8984 (pt0) REVERT: F 173 GLN cc_start: 0.9632 (tm-30) cc_final: 0.8908 (tm-30) REVERT: F 195 GLN cc_start: 0.9144 (pm20) cc_final: 0.8895 (pt0) REVERT: F 205 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8607 (mt-10) REVERT: F 227 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8776 (mm-30) REVERT: H 92 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9118 (tt) REVERT: H 166 GLU cc_start: 0.9347 (tp30) cc_final: 0.9104 (tp30) REVERT: H 173 GLN cc_start: 0.9389 (tm-30) cc_final: 0.9134 (tm-30) REVERT: H 195 GLN cc_start: 0.8540 (pp30) cc_final: 0.7958 (pp30) REVERT: I 38 THR cc_start: 0.9336 (p) cc_final: 0.9114 (p) REVERT: I 41 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7866 (pp20) REVERT: I 52 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8110 (ptp90) REVERT: I 56 GLN cc_start: 0.9527 (mt0) cc_final: 0.8990 (mt0) REVERT: J 80 GLN cc_start: 0.9641 (OUTLIER) cc_final: 0.9295 (tp40) REVERT: K 91 TYR cc_start: 0.8928 (t80) cc_final: 0.8554 (t80) REVERT: K 223 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9358 (mp) REVERT: L 14 GLN cc_start: 0.8864 (pt0) cc_final: 0.8553 (pt0) REVERT: L 34 LEU cc_start: 0.9711 (tp) cc_final: 0.9421 (pp) REVERT: L 166 GLU cc_start: 0.9417 (tp30) cc_final: 0.9069 (tp30) REVERT: L 188 LYS cc_start: 0.9418 (mmmm) cc_final: 0.8803 (tppp) outliers start: 85 outliers final: 63 residues processed: 342 average time/residue: 0.1605 time to fit residues: 81.4517 Evaluate side-chains 326 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 257 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 52 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 31 PHE Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 173 GLN Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 7 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 HIS H 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.064816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.052513 restraints weight = 84343.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.053991 restraints weight = 38194.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.055010 restraints weight = 23046.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.055687 restraints weight = 16507.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.056068 restraints weight = 13162.886| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.8677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19044 Z= 0.155 Angle : 0.636 15.236 25872 Z= 0.314 Chirality : 0.039 0.228 2952 Planarity : 0.004 0.038 3096 Dihedral : 4.370 43.872 2446 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.97 % Allowed : 23.38 % Favored : 72.65 % 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: 2.45 (0.18), residues: 2220 helix: 2.78 (0.12), residues: 1668 sheet: -1.92 (0.34), residues: 204 loop : -2.12 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 52 TYR 0.036 0.001 TYR H 65 PHE 0.019 0.001 PHE I 232 TRP 0.020 0.001 TRP C 44 HIS 0.007 0.001 HIS F 194 Details of bonding type rmsd covalent geometry : bond 0.00357 (19008) covalent geometry : angle 0.63456 (25800) SS BOND : bond 0.00297 ( 36) SS BOND : angle 1.03344 ( 72) hydrogen bonds : bond 0.03053 ( 1392) hydrogen bonds : angle 3.27189 ( 4176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 263 time to evaluate : 0.769 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: A 52 ARG cc_start: 0.7659 (mpp-170) cc_final: 0.7291 (mtm-85) REVERT: A 61 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8295 (mm-30) REVERT: A 91 TYR cc_start: 0.8804 (t80) cc_final: 0.8501 (t80) REVERT: B 56 GLN cc_start: 0.9431 (mt0) cc_final: 0.8658 (mt0) REVERT: B 91 TYR cc_start: 0.8675 (t80) cc_final: 0.8281 (t80) REVERT: B 195 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7928 (pp30) REVERT: C 48 GLN cc_start: 0.9474 (tp40) cc_final: 0.9196 (tp40) REVERT: C 160 LEU cc_start: 0.9670 (tp) cc_final: 0.9360 (pp) REVERT: D 34 LEU cc_start: 0.9690 (OUTLIER) cc_final: 0.9376 (pp) REVERT: D 48 GLN cc_start: 0.9472 (tp40) cc_final: 0.9186 (tp40) REVERT: D 188 LYS cc_start: 0.9190 (mmmm) cc_final: 0.8844 (mmmm) REVERT: E 56 GLN cc_start: 0.9460 (mt0) cc_final: 0.8320 (mt0) REVERT: F 52 ARG cc_start: 0.7832 (mtm110) cc_final: 0.6890 (mtm110) REVERT: F 56 GLN cc_start: 0.9280 (pt0) cc_final: 0.8968 (pt0) REVERT: F 173 GLN cc_start: 0.9631 (tm-30) cc_final: 0.8886 (tm-30) REVERT: F 195 GLN cc_start: 0.9168 (pm20) cc_final: 0.8898 (pt0) REVERT: F 205 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8574 (mt-10) REVERT: F 227 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8799 (mm-30) REVERT: G 41 GLU cc_start: 0.8409 (pm20) cc_final: 0.8132 (pm20) REVERT: H 92 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9135 (tt) REVERT: H 166 GLU cc_start: 0.9352 (tp30) cc_final: 0.9108 (tp30) REVERT: H 173 GLN cc_start: 0.9401 (tm-30) cc_final: 0.9143 (tm-30) REVERT: H 195 GLN cc_start: 0.8563 (pp30) cc_final: 0.7898 (pp30) REVERT: I 52 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8103 (ptp90) REVERT: I 56 GLN cc_start: 0.9530 (mt0) cc_final: 0.9026 (mt0) REVERT: K 91 TYR cc_start: 0.8948 (t80) cc_final: 0.8546 (t80) REVERT: K 173 GLN cc_start: 0.9590 (OUTLIER) cc_final: 0.9191 (tm-30) REVERT: K 223 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9377 (mp) REVERT: L 14 GLN cc_start: 0.8861 (pt0) cc_final: 0.8554 (pt0) REVERT: L 34 LEU cc_start: 0.9709 (tp) cc_final: 0.9413 (pp) REVERT: L 166 GLU cc_start: 0.9398 (tp30) cc_final: 0.9088 (tp30) REVERT: L 188 LYS cc_start: 0.9419 (mmmm) cc_final: 0.8790 (tppp) outliers start: 81 outliers final: 68 residues processed: 323 average time/residue: 0.1571 time to fit residues: 75.5715 Evaluate side-chains 329 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 255 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain D residue 16 TYR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 52 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 31 PHE Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 173 GLN Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 118 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 77 optimal weight: 0.4980 chunk 203 optimal weight: 0.5980 chunk 104 optimal weight: 0.0050 chunk 28 optimal weight: 20.0000 overall best weight: 2.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN ** G 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN K 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.065325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.053039 restraints weight = 84127.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.054531 restraints weight = 37971.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.055569 restraints weight = 22756.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.056012 restraints weight = 16159.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.056577 restraints weight = 13558.591| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.8811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19044 Z= 0.119 Angle : 0.658 16.671 25872 Z= 0.316 Chirality : 0.038 0.350 2952 Planarity : 0.004 0.038 3096 Dihedral : 4.329 48.146 2446 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.87 % Allowed : 23.33 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.18), residues: 2220 helix: 2.72 (0.12), residues: 1680 sheet: -1.85 (0.34), residues: 204 loop : -1.99 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 52 TYR 0.024 0.001 TYR I 91 PHE 0.018 0.001 PHE I 232 TRP 0.020 0.001 TRP J 44 HIS 0.005 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00274 (19008) covalent geometry : angle 0.65707 (25800) SS BOND : bond 0.00282 ( 36) SS BOND : angle 0.93326 ( 72) hydrogen bonds : bond 0.02978 ( 1392) hydrogen bonds : angle 3.23641 ( 4176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 279 time to evaluate : 0.784 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: A 52 ARG cc_start: 0.7626 (mpp-170) cc_final: 0.7262 (mtm-85) REVERT: A 61 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8331 (mm-30) REVERT: A 91 TYR cc_start: 0.8801 (t80) cc_final: 0.8473 (t80) REVERT: B 56 GLN cc_start: 0.9436 (mt0) cc_final: 0.8326 (mt0) REVERT: B 61 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8438 (mm-30) REVERT: B 91 TYR cc_start: 0.8693 (t80) cc_final: 0.8270 (t80) REVERT: B 188 LYS cc_start: 0.9115 (mmmm) cc_final: 0.8866 (mmmm) REVERT: C 48 GLN cc_start: 0.9424 (tp40) cc_final: 0.9221 (tp40) REVERT: C 56 GLN cc_start: 0.9575 (mt0) cc_final: 0.8755 (mt0) REVERT: C 160 LEU cc_start: 0.9654 (tp) cc_final: 0.9358 (pp) REVERT: D 34 LEU cc_start: 0.9694 (OUTLIER) cc_final: 0.9249 (pp) REVERT: D 48 GLN cc_start: 0.9427 (tp40) cc_final: 0.9167 (tp40) REVERT: D 56 GLN cc_start: 0.9457 (mt0) cc_final: 0.8477 (mt0) REVERT: D 188 LYS cc_start: 0.9209 (mmmm) cc_final: 0.8860 (mmmm) REVERT: F 56 GLN cc_start: 0.9237 (pt0) cc_final: 0.8937 (pt0) REVERT: F 173 GLN cc_start: 0.9621 (tm-30) cc_final: 0.8884 (tm-30) REVERT: F 195 GLN cc_start: 0.9148 (pm20) cc_final: 0.8931 (pt0) REVERT: F 205 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8640 (mp0) REVERT: F 227 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8812 (mm-30) REVERT: G 41 GLU cc_start: 0.8417 (pm20) cc_final: 0.8201 (pm20) REVERT: G 63 VAL cc_start: 0.9522 (m) cc_final: 0.9273 (p) REVERT: H 89 LEU cc_start: 0.9481 (tt) cc_final: 0.9240 (mm) REVERT: H 92 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9131 (tt) REVERT: H 166 GLU cc_start: 0.9349 (tp30) cc_final: 0.9114 (tp30) REVERT: H 173 GLN cc_start: 0.9380 (tm-30) cc_final: 0.9128 (tm-30) REVERT: H 195 GLN cc_start: 0.8551 (pp30) cc_final: 0.7927 (pp30) REVERT: I 56 GLN cc_start: 0.9493 (mt0) cc_final: 0.9002 (mt0) REVERT: K 91 TYR cc_start: 0.8942 (t80) cc_final: 0.8526 (t80) REVERT: K 173 GLN cc_start: 0.9595 (OUTLIER) cc_final: 0.9187 (tm-30) REVERT: K 205 GLU cc_start: 0.9282 (tp30) cc_final: 0.8733 (mm-30) REVERT: L 14 GLN cc_start: 0.8851 (pt0) cc_final: 0.8530 (pt0) REVERT: L 34 LEU cc_start: 0.9705 (tp) cc_final: 0.9408 (pp) REVERT: L 166 GLU cc_start: 0.9392 (tp30) cc_final: 0.9089 (tp30) REVERT: L 188 LYS cc_start: 0.9418 (mmmm) cc_final: 0.8776 (tppp) outliers start: 79 outliers final: 67 residues processed: 334 average time/residue: 0.1531 time to fit residues: 76.4158 Evaluate side-chains 333 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 263 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 52 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 31 PHE Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 173 GLN Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN J 195 GLN K 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.064402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.052253 restraints weight = 84818.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.053737 restraints weight = 38106.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.054754 restraints weight = 22882.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.055286 restraints weight = 16200.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.055902 restraints weight = 13329.033| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.9062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19044 Z= 0.156 Angle : 0.667 15.868 25872 Z= 0.326 Chirality : 0.039 0.395 2952 Planarity : 0.004 0.038 3096 Dihedral : 4.352 53.162 2446 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.87 % Allowed : 23.73 % Favored : 72.40 % 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: 2.48 (0.18), residues: 2220 helix: 2.72 (0.12), residues: 1680 sheet: -1.82 (0.34), residues: 204 loop : -1.92 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 52 TYR 0.038 0.001 TYR H 65 PHE 0.031 0.001 PHE J 165 TRP 0.025 0.001 TRP J 44 HIS 0.005 0.001 HIS F 194 Details of bonding type rmsd covalent geometry : bond 0.00358 (19008) covalent geometry : angle 0.66538 (25800) SS BOND : bond 0.00343 ( 36) SS BOND : angle 1.01038 ( 72) hydrogen bonds : bond 0.03054 ( 1392) hydrogen bonds : angle 3.30677 ( 4176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 266 time to evaluate : 0.749 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: A 52 ARG cc_start: 0.7629 (mpp-170) cc_final: 0.7251 (mtm-85) REVERT: A 61 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8331 (mm-30) REVERT: A 91 TYR cc_start: 0.8858 (t80) cc_final: 0.8525 (t80) REVERT: B 56 GLN cc_start: 0.9472 (mt0) cc_final: 0.8721 (mt0) REVERT: B 91 TYR cc_start: 0.8747 (t80) cc_final: 0.8295 (t80) REVERT: B 195 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7772 (pp30) REVERT: C 34 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9208 (pp) REVERT: C 48 GLN cc_start: 0.9458 (tp40) cc_final: 0.9206 (tp40) REVERT: C 56 GLN cc_start: 0.9593 (mt0) cc_final: 0.8786 (mt0) REVERT: C 61 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8441 (mm-30) REVERT: C 160 LEU cc_start: 0.9670 (tp) cc_final: 0.9377 (pp) REVERT: C 188 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8602 (tppp) REVERT: D 34 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9249 (pp) REVERT: D 188 LYS cc_start: 0.9223 (mmmm) cc_final: 0.8859 (mmmm) REVERT: E 61 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8254 (mm-30) REVERT: F 56 GLN cc_start: 0.9315 (pt0) cc_final: 0.9021 (pt0) REVERT: F 173 GLN cc_start: 0.9625 (tm-30) cc_final: 0.8858 (tm-30) REVERT: F 195 GLN cc_start: 0.9183 (pm20) cc_final: 0.8921 (pt0) REVERT: F 227 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8835 (mm-30) REVERT: G 41 GLU cc_start: 0.8449 (pm20) cc_final: 0.8222 (pm20) REVERT: H 89 LEU cc_start: 0.9511 (tt) cc_final: 0.9300 (mm) REVERT: H 92 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9130 (tt) REVERT: H 166 GLU cc_start: 0.9351 (tp30) cc_final: 0.9107 (tp30) REVERT: H 173 GLN cc_start: 0.9407 (tm-30) cc_final: 0.9140 (tm-30) REVERT: H 195 GLN cc_start: 0.8605 (pp30) cc_final: 0.8262 (pp30) REVERT: I 52 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8109 (ptp90) REVERT: I 56 GLN cc_start: 0.9522 (mt0) cc_final: 0.9065 (mt0) REVERT: K 30 ILE cc_start: 0.9503 (mm) cc_final: 0.9276 (tp) REVERT: K 91 TYR cc_start: 0.8952 (t80) cc_final: 0.8502 (t80) REVERT: K 173 GLN cc_start: 0.9599 (OUTLIER) cc_final: 0.9180 (tm-30) REVERT: K 223 LEU cc_start: 0.9654 (OUTLIER) cc_final: 0.9406 (mp) REVERT: L 14 GLN cc_start: 0.8840 (pt0) cc_final: 0.8516 (pt0) REVERT: L 34 LEU cc_start: 0.9722 (tp) cc_final: 0.9436 (pp) REVERT: L 166 GLU cc_start: 0.9388 (tp30) cc_final: 0.9087 (tp30) REVERT: L 188 LYS cc_start: 0.9431 (mmmm) cc_final: 0.8806 (tppp) outliers start: 79 outliers final: 64 residues processed: 325 average time/residue: 0.1490 time to fit residues: 72.5550 Evaluate side-chains 328 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 257 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 52 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 31 PHE Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 173 GLN Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 72 optimal weight: 50.0000 chunk 94 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 40.0000 chunk 99 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 206 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN H 224 ASN ** J 195 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 = 0.3278 r_free = 0.3278 target = 0.064517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.052327 restraints weight = 85624.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.053817 restraints weight = 38349.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.054734 restraints weight = 23058.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.055466 restraints weight = 16773.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.055625 restraints weight = 13316.562| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.9059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.246 19044 Z= 0.205 Angle : 0.827 59.200 25872 Z= 0.442 Chirality : 0.040 0.643 2952 Planarity : 0.004 0.038 3096 Dihedral : 4.354 53.199 2446 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.82 % Allowed : 23.73 % Favored : 72.45 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.18), residues: 2220 helix: 2.71 (0.12), residues: 1680 sheet: -1.81 (0.34), residues: 204 loop : -1.93 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 52 TYR 0.027 0.001 TYR H 65 PHE 0.028 0.001 PHE J 165 TRP 0.022 0.001 TRP J 44 HIS 0.005 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00460 (19008) covalent geometry : angle 0.82602 (25800) SS BOND : bond 0.00320 ( 36) SS BOND : angle 0.99936 ( 72) hydrogen bonds : bond 0.03061 ( 1392) hydrogen bonds : angle 3.31211 ( 4176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3006.49 seconds wall clock time: 53 minutes 10.55 seconds (3190.55 seconds total)