Starting phenix.real_space_refine on Mon May 19 10:37:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qko_18468/05_2025/8qko_18468_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qko_18468/05_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_18468/05_2025/8qko_18468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qko_18468/05_2025/8qko_18468.map" model { file = "/net/cci-nas-00/data/ceres_data/8qko_18468/05_2025/8qko_18468_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qko_18468/05_2025/8qko_18468_neut.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.90, per 1000 atoms: 0.59 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: 4.62 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.57 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: 5.89 Time building geometry restraints manager: 5.48 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 41.060 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.730 ------------------------------------------------------------------------------- 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 : 9.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP A 77 HIS 0.003 0.001 HIS E 73 PHE 0.013 0.001 PHE G 31 TYR 0.005 0.001 TYR K 155 ARG 0.004 0.001 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.11078 ( 1392) hydrogen bonds : angle 4.24420 ( 4176) SS BOND : bond 0.00247 ( 36) SS BOND : angle 0.65984 ( 72) covalent geometry : bond 0.00317 (19008) covalent geometry : angle 0.52212 (25800) *********************** 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 : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.9310 (mt0) cc_final: 0.8788 (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: 0.6682 (p0) REVERT: C 76 PHE cc_start: 0.7676 (t80) cc_final: 0.7319 (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: 0.8282 (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: 0.8370 (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: 0.7944 (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: 0.7294 (pttm) REVERT: G 25 LEU cc_start: 0.9447 (mt) cc_final: 0.9209 (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: 0.5949 (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: 0.6857 (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: 0.8707 (p) REVERT: J 231 VAL cc_start: 0.9085 (t) cc_final: 0.8774 (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: 0.8254 (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: 0.9239 (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: 0.3188 time to fit residues: 295.1574 Evaluate side-chains 364 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 347 time to evaluate : 1.985 ------------------------------------------------------------------------------- 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 182 optimal weight: 3.9990 chunk 163 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 40.0000 chunk 110 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 196 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 54 ASN 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 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN K 48 GLN K 56 GLN K 73 HIS ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 173 GLN ** L 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 224 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.076167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.063175 restraints weight = 81140.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.064890 restraints weight = 41240.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066076 restraints weight = 25598.271| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 19044 Z= 0.164 Angle : 0.653 10.845 25872 Z= 0.325 Chirality : 0.040 0.226 2952 Planarity : 0.004 0.051 3096 Dihedral : 5.271 49.322 2483 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.48 % Allowed : 14.36 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.17), residues: 2220 helix: 2.57 (0.11), residues: 1668 sheet: -1.61 (0.33), residues: 204 loop : -2.00 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP J 24 HIS 0.007 0.001 HIS G 73 PHE 0.027 0.002 PHE G 165 TYR 0.018 0.001 TYR D 91 ARG 0.007 0.001 ARG F 202 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 1392) hydrogen bonds : angle 3.34663 ( 4176) SS BOND : bond 0.00505 ( 36) SS BOND : angle 1.83411 ( 72) covalent geometry : bond 0.00381 (19008) covalent geometry : angle 0.64640 (25800) *********************** 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 455 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 384 time to evaluate : 2.200 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 56 GLN cc_start: 0.9292 (mt0) cc_final: 0.8728 (mt0) REVERT: A 61 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8341 (mm-30) REVERT: A 91 TYR cc_start: 0.8603 (t80) cc_final: 0.8360 (t80) REVERT: B 48 GLN cc_start: 0.9561 (OUTLIER) cc_final: 0.9049 (tp40) REVERT: B 61 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7886 (mm-30) REVERT: B 65 TYR cc_start: 0.9229 (t80) cc_final: 0.8972 (t80) REVERT: B 91 TYR cc_start: 0.8446 (t80) cc_final: 0.8205 (t80) REVERT: C 46 ASP cc_start: 0.7241 (p0) cc_final: 0.6948 (p0) REVERT: C 61 GLU cc_start: 0.7829 (mp0) cc_final: 0.7503 (mm-30) REVERT: C 164 ILE cc_start: 0.9344 (mm) cc_final: 0.9004 (pt) REVERT: D 41 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7697 (mt-10) REVERT: D 53 CYS cc_start: 0.5101 (OUTLIER) cc_final: 0.3888 (p) REVERT: D 164 ILE cc_start: 0.8945 (mm) cc_final: 0.8526 (pt) REVERT: E 22 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7300 (mttp) REVERT: E 47 GLU cc_start: 0.8176 (tp30) cc_final: 0.7171 (tp30) REVERT: E 56 GLN cc_start: 0.9414 (mt0) cc_final: 0.9062 (mt0) REVERT: F 52 ARG cc_start: 0.7490 (mtm-85) cc_final: 0.7077 (mtm-85) REVERT: F 56 GLN cc_start: 0.8478 (pt0) cc_final: 0.7913 (pt0) REVERT: F 173 GLN cc_start: 0.9384 (tm-30) cc_final: 0.8874 (tm-30) REVERT: F 227 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8237 (mm-30) REVERT: G 25 LEU cc_start: 0.9494 (mt) cc_final: 0.9207 (pp) REVERT: G 63 VAL cc_start: 0.9284 (m) cc_final: 0.9072 (p) REVERT: H 41 GLU cc_start: 0.8574 (tp30) cc_final: 0.8193 (tm-30) REVERT: H 99 MET cc_start: 0.8899 (mmp) cc_final: 0.8367 (mmp) REVERT: H 166 GLU cc_start: 0.9211 (tp30) cc_final: 0.8855 (tp30) REVERT: H 173 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8743 (tm-30) REVERT: H 205 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7641 (mp0) REVERT: I 188 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8740 (mmmm) REVERT: J 56 GLN cc_start: 0.8701 (mt0) cc_final: 0.8404 (mt0) REVERT: J 212 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8492 (t80) REVERT: K 173 GLN cc_start: 0.9258 (tm-30) cc_final: 0.8695 (pp30) REVERT: L 67 LYS cc_start: 0.8959 (tppt) cc_final: 0.8751 (ttmm) REVERT: L 80 GLN cc_start: 0.8836 (tt0) cc_final: 0.8302 (tt0) REVERT: L 188 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8582 (mptt) REVERT: L 218 LEU cc_start: 0.9585 (mm) cc_final: 0.9342 (mm) outliers start: 71 outliers final: 42 residues processed: 429 average time/residue: 0.2982 time to fit residues: 193.5161 Evaluate side-chains 364 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 318 time to evaluate : 2.259 ------------------------------------------------------------------------------- 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 89 LEU 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 E residue 16 TYR Chi-restraints excluded: chain E residue 22 LYS 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 E residue 220 SER 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 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 I residue 78 VAL 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 223 LEU Chi-restraints excluded: chain J residue 224 ASN Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 48 GLN Chi-restraints excluded: chain K residue 88 THR 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 203 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 48 GLN B 54 ASN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN D 80 GLN ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN K 194 HIS ** L 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.072298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.059691 restraints weight = 82223.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.061317 restraints weight = 40603.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.062514 restraints weight = 25052.690| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19044 Z= 0.174 Angle : 0.645 13.698 25872 Z= 0.327 Chirality : 0.040 0.235 2952 Planarity : 0.004 0.051 3096 Dihedral : 4.813 59.504 2457 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.36 % Allowed : 16.72 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.17), residues: 2220 helix: 2.55 (0.11), residues: 1668 sheet: -1.70 (0.33), residues: 204 loop : -1.96 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 44 HIS 0.006 0.001 HIS H 194 PHE 0.036 0.001 PHE G 165 TYR 0.025 0.001 TYR E 65 ARG 0.007 0.001 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 1392) hydrogen bonds : angle 3.29193 ( 4176) SS BOND : bond 0.00394 ( 36) SS BOND : angle 1.54756 ( 72) covalent geometry : bond 0.00400 (19008) covalent geometry : angle 0.64100 (25800) *********************** 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 427 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 338 time to evaluate : 2.004 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: 0.8516 (p0) cc_final: 0.7905 (p0) REVERT: A 61 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8413 (tp30) REVERT: A 91 TYR cc_start: 0.8684 (t80) cc_final: 0.8310 (t80) REVERT: B 56 GLN cc_start: 0.9414 (mt0) cc_final: 0.8770 (mt0) REVERT: C 38 THR cc_start: 0.8721 (t) cc_final: 0.8476 (t) REVERT: C 47 GLU cc_start: 0.7951 (pt0) cc_final: 0.7691 (pt0) REVERT: C 179 PHE cc_start: 0.8067 (m-80) cc_final: 0.7508 (m-80) REVERT: D 41 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7954 (mt-10) REVERT: E 47 GLU cc_start: 0.8723 (tp30) cc_final: 0.8156 (tp30) REVERT: E 56 GLN cc_start: 0.9490 (mt0) cc_final: 0.9115 (mt0) REVERT: E 65 TYR cc_start: 0.8765 (t80) cc_final: 0.8227 (t80) REVERT: F 56 GLN cc_start: 0.8826 (pt0) cc_final: 0.8299 (pt0) REVERT: F 71 ILE cc_start: 0.9440 (pt) cc_final: 0.9209 (tp) REVERT: F 173 GLN cc_start: 0.9541 (tm-30) cc_final: 0.8903 (tm-30) REVERT: F 195 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8756 (mp10) REVERT: F 205 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8402 (mt-10) REVERT: F 227 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8431 (mm-30) REVERT: G 32 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8547 (ptp-110) REVERT: G 41 GLU cc_start: 0.8398 (pp20) cc_final: 0.8180 (pp20) REVERT: G 66 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8740 (m-30) REVERT: G 165 PHE cc_start: 0.8051 (m-80) cc_final: 0.7808 (m-80) REVERT: H 8 LYS cc_start: 0.9651 (pttp) cc_final: 0.9383 (ptpp) REVERT: H 41 GLU cc_start: 0.8724 (tp30) cc_final: 0.8411 (tm-30) REVERT: H 166 GLU cc_start: 0.9300 (tp30) cc_final: 0.8993 (tp30) REVERT: H 173 GLN cc_start: 0.9190 (tm-30) cc_final: 0.8871 (tm-30) REVERT: I 58 PRO cc_start: 0.8877 (Cg_exo) cc_final: 0.8523 (Cg_endo) REVERT: I 75 ARG cc_start: 0.9036 (mpp80) cc_final: 0.8198 (mmt90) REVERT: I 188 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8879 (mmmm) REVERT: J 52 ARG cc_start: 0.8708 (ptp90) cc_final: 0.8334 (mpp80) REVERT: J 56 GLN cc_start: 0.8894 (mt0) cc_final: 0.8258 (mt0) REVERT: J 75 ARG cc_start: 0.9079 (mpp80) cc_final: 0.8402 (mtt-85) REVERT: J 212 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8836 (t80) REVERT: K 14 GLN cc_start: 0.8483 (pt0) cc_final: 0.7933 (pt0) REVERT: K 162 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8096 (mttp) REVERT: K 173 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8922 (tm-30) REVERT: L 48 GLN cc_start: 0.8095 (pm20) cc_final: 0.7352 (tt0) REVERT: L 218 LEU cc_start: 0.9635 (mm) cc_final: 0.9413 (mm) outliers start: 89 outliers final: 55 residues processed: 395 average time/residue: 0.2875 time to fit residues: 172.0218 Evaluate side-chains 348 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 289 time to evaluate : 1.962 ------------------------------------------------------------------------------- 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 40 VAL 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 55 THR Chi-restraints excluded: chain D residue 61 GLU 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 71 ILE 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 E residue 201 SER Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 195 GLN 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 66 ASP 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 G residue 160 LEU Chi-restraints excluded: chain G residue 195 GLN 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 49 SER Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 47 GLU 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 223 LEU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 27 optimal weight: 5.9990 chunk 163 optimal weight: 30.0000 chunk 144 optimal weight: 50.0000 chunk 105 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 55 optimal weight: 40.0000 chunk 39 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** A 224 ASN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN D 54 ASN F 48 GLN ** H 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 ASN K 48 GLN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.068327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.055457 restraints weight = 82791.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.057028 restraints weight = 39455.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.058008 restraints weight = 24112.079| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.6483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 19044 Z= 0.220 Angle : 0.635 11.184 25872 Z= 0.324 Chirality : 0.039 0.195 2952 Planarity : 0.004 0.032 3096 Dihedral : 4.796 52.235 2450 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.85 % Allowed : 19.41 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.17), residues: 2220 helix: 2.60 (0.11), residues: 1668 sheet: -1.83 (0.33), residues: 204 loop : -2.04 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 44 HIS 0.007 0.001 HIS L 194 PHE 0.025 0.001 PHE G 165 TYR 0.022 0.001 TYR D 65 ARG 0.005 0.001 ARG C 100 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 1392) hydrogen bonds : angle 3.35513 ( 4176) SS BOND : bond 0.00345 ( 36) SS BOND : angle 1.30636 ( 72) covalent geometry : bond 0.00471 (19008) covalent geometry : angle 0.63240 (25800) *********************** 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 405 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 306 time to evaluate : 2.014 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: 0.8057 (mtm-85) cc_final: 0.7642 (mtm-85) REVERT: B 56 GLN cc_start: 0.9431 (mt0) cc_final: 0.8695 (mt0) REVERT: C 61 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7733 (mm-30) REVERT: C 160 LEU cc_start: 0.9564 (tp) cc_final: 0.9242 (tt) REVERT: C 188 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8669 (mmmm) REVERT: E 47 GLU cc_start: 0.8751 (tp30) cc_final: 0.8314 (tp30) REVERT: E 56 GLN cc_start: 0.9520 (mt0) cc_final: 0.9094 (mt0) REVERT: E 65 TYR cc_start: 0.9258 (t80) cc_final: 0.8556 (t80) REVERT: E 227 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8930 (mm-30) REVERT: F 48 GLN cc_start: 0.9560 (OUTLIER) cc_final: 0.9080 (tp40) REVERT: F 56 GLN cc_start: 0.9146 (pt0) cc_final: 0.8651 (pt0) REVERT: F 173 GLN cc_start: 0.9612 (tm-30) cc_final: 0.9002 (tm-30) REVERT: F 195 GLN cc_start: 0.9179 (pm20) cc_final: 0.8837 (mp10) REVERT: F 205 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8515 (mt-10) REVERT: F 227 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8748 (mm-30) REVERT: G 47 GLU cc_start: 0.8182 (mp0) cc_final: 0.7981 (pm20) REVERT: G 61 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7633 (tm-30) REVERT: G 165 PHE cc_start: 0.8390 (m-80) cc_final: 0.8011 (m-80) REVERT: H 41 GLU cc_start: 0.8771 (tp30) cc_final: 0.8502 (tm-30) REVERT: H 65 TYR cc_start: 0.9354 (t80) cc_final: 0.9117 (t80) REVERT: H 166 GLU cc_start: 0.9345 (tp30) cc_final: 0.8984 (tp30) REVERT: H 173 GLN cc_start: 0.9303 (tm-30) cc_final: 0.9079 (tm-30) REVERT: I 56 GLN cc_start: 0.9451 (mm-40) cc_final: 0.8945 (mp10) REVERT: I 188 LYS cc_start: 0.9328 (mmmm) cc_final: 0.9082 (mmmm) REVERT: J 56 GLN cc_start: 0.9123 (mt0) cc_final: 0.8532 (mt0) REVERT: J 75 ARG cc_start: 0.9284 (mpp80) cc_final: 0.8405 (mtt-85) REVERT: K 46 ASP cc_start: 0.8563 (p0) cc_final: 0.8314 (p0) REVERT: K 166 GLU cc_start: 0.9111 (tp30) cc_final: 0.8820 (tp30) REVERT: K 173 GLN cc_start: 0.9299 (tm-30) cc_final: 0.8851 (tm-30) REVERT: K 205 GLU cc_start: 0.9260 (tp30) cc_final: 0.9030 (tp30) REVERT: L 48 GLN cc_start: 0.8371 (pm20) cc_final: 0.8096 (tt0) REVERT: L 188 LYS cc_start: 0.9359 (mmmm) cc_final: 0.8760 (tppp) outliers start: 99 outliers final: 66 residues processed: 369 average time/residue: 0.3023 time to fit residues: 166.1195 Evaluate side-chains 343 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 276 time to evaluate : 2.201 ------------------------------------------------------------------------------- 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 89 LEU Chi-restraints excluded: chain C residue 154 THR 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 E residue 16 TYR 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 81 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 86 VAL 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 63 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 23 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 55 THR 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 86 VAL Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain J residue 16 TYR 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 218 LEU Chi-restraints excluded: chain J residue 223 LEU 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 47 GLU Chi-restraints excluded: chain K residue 86 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 L residue 23 VAL Chi-restraints excluded: chain L residue 55 THR 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 35 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 100 optimal weight: 0.2980 chunk 23 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 105 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- 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 224 ASN H 194 HIS ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 GLN J 224 ASN K 195 GLN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.067824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.054993 restraints weight = 83642.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.056501 restraints weight = 39334.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.057552 restraints weight = 23772.539| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.7123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19044 Z= 0.143 Angle : 0.606 13.771 25872 Z= 0.300 Chirality : 0.037 0.207 2952 Planarity : 0.004 0.036 3096 Dihedral : 4.614 54.478 2450 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.56 % Allowed : 20.20 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.17), residues: 2220 helix: 2.80 (0.11), residues: 1668 sheet: -1.75 (0.34), residues: 204 loop : -2.20 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 24 HIS 0.005 0.001 HIS K 73 PHE 0.027 0.001 PHE G 165 TYR 0.014 0.001 TYR F 65 ARG 0.005 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03101 ( 1392) hydrogen bonds : angle 3.20854 ( 4176) SS BOND : bond 0.00313 ( 36) SS BOND : angle 1.18195 ( 72) covalent geometry : bond 0.00330 (19008) covalent geometry : angle 0.60377 (25800) *********************** 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 398 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 305 time to evaluate : 2.114 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: B 56 GLN cc_start: 0.9391 (mt0) cc_final: 0.8610 (mt0) REVERT: C 61 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7948 (mm-30) REVERT: C 160 LEU cc_start: 0.9573 (tp) cc_final: 0.9280 (tt) REVERT: D 41 GLU cc_start: 0.8122 (pm20) cc_final: 0.7907 (pm20) REVERT: D 56 GLN cc_start: 0.9453 (mt0) cc_final: 0.9197 (mt0) REVERT: D 171 LEU cc_start: 0.9540 (tp) cc_final: 0.9278 (tt) REVERT: D 188 LYS cc_start: 0.9107 (mmmm) cc_final: 0.8675 (mmmm) REVERT: E 47 GLU cc_start: 0.8714 (tp30) cc_final: 0.8367 (tp30) REVERT: E 56 GLN cc_start: 0.9459 (mt0) cc_final: 0.9192 (mt0) REVERT: E 65 TYR cc_start: 0.9290 (t80) cc_final: 0.8617 (t80) REVERT: F 56 GLN cc_start: 0.9169 (pt0) cc_final: 0.8914 (pt0) REVERT: F 166 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8952 (tm-30) REVERT: F 173 GLN cc_start: 0.9616 (tm-30) cc_final: 0.8915 (tm-30) REVERT: F 195 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8927 (pt0) REVERT: F 205 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8619 (mt-10) REVERT: F 227 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8791 (mm-30) REVERT: G 34 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9344 (pp) REVERT: G 47 GLU cc_start: 0.8208 (mp0) cc_final: 0.7971 (pm20) REVERT: G 165 PHE cc_start: 0.8544 (m-80) cc_final: 0.8123 (m-80) REVERT: H 8 LYS cc_start: 0.9686 (pttp) cc_final: 0.9429 (ptpp) REVERT: H 41 GLU cc_start: 0.8819 (tp30) cc_final: 0.8561 (tm-30) REVERT: H 92 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9001 (tt) REVERT: H 166 GLU cc_start: 0.9343 (tp30) cc_final: 0.8954 (tp30) REVERT: H 173 GLN cc_start: 0.9281 (tm-30) cc_final: 0.9047 (tm-30) REVERT: I 47 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7777 (mm-30) REVERT: I 165 PHE cc_start: 0.8502 (m-80) cc_final: 0.8146 (m-80) REVERT: J 205 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8914 (mm-30) REVERT: K 83 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.9186 (t80) REVERT: K 166 GLU cc_start: 0.9153 (tp30) cc_final: 0.8872 (tp30) REVERT: K 173 GLN cc_start: 0.9356 (tm-30) cc_final: 0.8885 (tm-30) REVERT: K 205 GLU cc_start: 0.9298 (tp30) cc_final: 0.9033 (tp30) REVERT: L 14 GLN cc_start: 0.8923 (pt0) cc_final: 0.8596 (pt0) REVERT: L 47 GLU cc_start: 0.8556 (pm20) cc_final: 0.8122 (pm20) REVERT: L 67 LYS cc_start: 0.9190 (tppt) cc_final: 0.8913 (tptp) REVERT: L 166 GLU cc_start: 0.9414 (tp30) cc_final: 0.9091 (tp30) REVERT: L 188 LYS cc_start: 0.9432 (mmmm) cc_final: 0.8801 (tppp) outliers start: 93 outliers final: 59 residues processed: 364 average time/residue: 0.2991 time to fit residues: 163.5015 Evaluate side-chains 339 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 276 time to evaluate : 2.070 ------------------------------------------------------------------------------- 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 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 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 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 36 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 201 SER 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 49 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 213 MET 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 182 SER 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 92 LEU 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 83 PHE Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 52 ARG 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 35 LEU Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 83 PHE Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 ASP 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 135 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 186 optimal weight: 0.0470 chunk 73 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- 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 ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN K 195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.066797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.054329 restraints weight = 85060.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.055871 restraints weight = 38940.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.056963 restraints weight = 23355.171| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.7448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19044 Z= 0.117 Angle : 0.618 14.335 25872 Z= 0.297 Chirality : 0.038 0.325 2952 Planarity : 0.003 0.037 3096 Dihedral : 4.320 44.642 2448 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.46 % Allowed : 21.47 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.18), residues: 2220 helix: 2.79 (0.11), residues: 1680 sheet: -1.75 (0.34), residues: 204 loop : -2.13 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 24 HIS 0.003 0.001 HIS G 73 PHE 0.025 0.001 PHE I 232 TYR 0.021 0.001 TYR F 65 ARG 0.006 0.000 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.02972 ( 1392) hydrogen bonds : angle 3.13451 ( 4176) SS BOND : bond 0.00382 ( 36) SS BOND : angle 0.99207 ( 72) covalent geometry : bond 0.00265 (19008) covalent geometry : angle 0.61679 (25800) *********************** 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 397 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 306 time to evaluate : 2.235 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: 0.8201 (mtm-85) cc_final: 0.7732 (mtm-85) REVERT: B 52 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7646 (mtm-85) REVERT: B 91 TYR cc_start: 0.8535 (t80) cc_final: 0.8304 (t80) REVERT: B 195 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7894 (pp30) REVERT: C 34 LEU cc_start: 0.9739 (tp) cc_final: 0.9250 (pp) REVERT: C 61 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7958 (mm-30) REVERT: C 160 LEU cc_start: 0.9593 (tp) cc_final: 0.9201 (pp) REVERT: C 166 GLU cc_start: 0.9022 (tp30) cc_final: 0.8782 (tm-30) REVERT: D 34 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9313 (pp) REVERT: D 46 ASP cc_start: 0.9279 (p0) cc_final: 0.8985 (p0) REVERT: D 56 GLN cc_start: 0.9459 (mt0) cc_final: 0.9198 (mt0) REVERT: D 171 LEU cc_start: 0.9585 (tp) cc_final: 0.9341 (tt) REVERT: D 188 LYS cc_start: 0.9145 (mmmm) cc_final: 0.8857 (mmmm) REVERT: E 47 GLU cc_start: 0.8645 (tp30) cc_final: 0.8339 (tp30) REVERT: E 56 GLN cc_start: 0.9447 (mt0) cc_final: 0.9187 (mt0) REVERT: E 65 TYR cc_start: 0.9290 (t80) cc_final: 0.8637 (t80) REVERT: F 56 GLN cc_start: 0.9134 (pt0) cc_final: 0.8778 (pt0) REVERT: F 91 TYR cc_start: 0.8050 (t80) cc_final: 0.7815 (t80) REVERT: F 166 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8938 (tm-30) REVERT: F 173 GLN cc_start: 0.9606 (tm-30) cc_final: 0.8903 (tm-30) REVERT: F 195 GLN cc_start: 0.9170 (pm20) cc_final: 0.8905 (pt0) REVERT: F 205 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8594 (mt-10) REVERT: F 227 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8847 (mm-30) REVERT: G 47 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7960 (pm20) REVERT: G 188 LYS cc_start: 0.8990 (mptt) cc_final: 0.8737 (mmmm) REVERT: H 8 LYS cc_start: 0.9669 (pttp) cc_final: 0.9416 (pttm) REVERT: H 41 GLU cc_start: 0.8816 (tp30) cc_final: 0.8596 (tm-30) REVERT: H 47 GLU cc_start: 0.8176 (pt0) cc_final: 0.7956 (pt0) REVERT: H 65 TYR cc_start: 0.9367 (t80) cc_final: 0.8858 (t80) REVERT: H 166 GLU cc_start: 0.9325 (tp30) cc_final: 0.8929 (tp30) REVERT: H 173 GLN cc_start: 0.9291 (tm-30) cc_final: 0.9038 (tm-30) REVERT: H 213 MET cc_start: 0.8897 (mmm) cc_final: 0.8661 (mmm) REVERT: I 47 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7766 (mm-30) REVERT: I 165 PHE cc_start: 0.8602 (m-80) cc_final: 0.8244 (m-80) REVERT: K 91 TYR cc_start: 0.8770 (t80) cc_final: 0.8493 (t80) REVERT: K 173 GLN cc_start: 0.9241 (tm-30) cc_final: 0.8868 (tm-30) REVERT: L 14 GLN cc_start: 0.8904 (pt0) cc_final: 0.8555 (pt0) REVERT: L 67 LYS cc_start: 0.9220 (tppt) cc_final: 0.8923 (tptp) REVERT: L 173 GLN cc_start: 0.9628 (OUTLIER) cc_final: 0.9394 (tt0) outliers start: 91 outliers final: 57 residues processed: 369 average time/residue: 0.3013 time to fit residues: 167.1195 Evaluate side-chains 345 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 284 time to evaluate : 1.993 ------------------------------------------------------------------------------- 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 18 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 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 192 CYS 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 36 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 31 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 47 GLU 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 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 86 VAL Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 83 PHE Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 52 ARG 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 35 LEU 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 184 VAL Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 173 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 135 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 chunk 19 optimal weight: 40.0000 chunk 105 optimal weight: 9.9990 chunk 109 optimal weight: 40.0000 chunk 50 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.065893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.053250 restraints weight = 84078.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.054704 restraints weight = 38341.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.055829 restraints weight = 23229.271| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.8063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19044 Z= 0.165 Angle : 0.629 14.340 25872 Z= 0.314 Chirality : 0.038 0.198 2952 Planarity : 0.004 0.036 3096 Dihedral : 4.315 41.002 2446 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.26 % Allowed : 22.11 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.18), residues: 2220 helix: 2.83 (0.11), residues: 1668 sheet: -1.76 (0.34), residues: 204 loop : -2.22 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 44 HIS 0.022 0.002 HIS B 194 PHE 0.020 0.001 PHE I 232 TYR 0.035 0.001 TYR F 65 ARG 0.006 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03097 ( 1392) hydrogen bonds : angle 3.21261 ( 4176) SS BOND : bond 0.00365 ( 36) SS BOND : angle 1.07308 ( 72) covalent geometry : bond 0.00380 (19008) covalent geometry : angle 0.62729 (25800) *********************** 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 377 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 290 time to evaluate : 2.357 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 52 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7499 (mtm-85) REVERT: B 56 GLN cc_start: 0.9421 (mt0) cc_final: 0.8635 (mt0) REVERT: B 91 TYR cc_start: 0.8636 (t80) cc_final: 0.8338 (t80) REVERT: B 188 LYS cc_start: 0.9162 (mmmm) cc_final: 0.8820 (mmmm) REVERT: B 195 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8002 (pp30) REVERT: C 34 LEU cc_start: 0.9744 (tp) cc_final: 0.9268 (pp) REVERT: C 160 LEU cc_start: 0.9643 (tp) cc_final: 0.9289 (pp) REVERT: D 34 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9365 (pp) REVERT: D 56 GLN cc_start: 0.9524 (mt0) cc_final: 0.8683 (mp10) REVERT: D 188 LYS cc_start: 0.9231 (mmmm) cc_final: 0.8906 (mmmm) REVERT: E 47 GLU cc_start: 0.8732 (tp30) cc_final: 0.8498 (tp30) REVERT: E 56 GLN cc_start: 0.9477 (mt0) cc_final: 0.9224 (mt0) REVERT: E 65 TYR cc_start: 0.9395 (t80) cc_final: 0.8839 (t80) REVERT: F 56 GLN cc_start: 0.9269 (pt0) cc_final: 0.8955 (pt0) REVERT: F 91 TYR cc_start: 0.8398 (t80) cc_final: 0.8111 (t80) REVERT: F 166 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8935 (tm-30) REVERT: F 173 GLN cc_start: 0.9618 (tm-30) cc_final: 0.8869 (tm-30) REVERT: F 195 GLN cc_start: 0.9234 (pm20) cc_final: 0.8864 (pt0) REVERT: F 205 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8671 (mt-10) REVERT: F 227 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8813 (mm-30) REVERT: G 47 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: G 56 GLN cc_start: 0.9531 (mm-40) cc_final: 0.9320 (mm-40) REVERT: H 41 GLU cc_start: 0.8847 (tp30) cc_final: 0.8634 (tm-30) REVERT: H 47 GLU cc_start: 0.8215 (pt0) cc_final: 0.7991 (pt0) REVERT: H 65 TYR cc_start: 0.9479 (t80) cc_final: 0.9191 (t80) REVERT: H 92 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9085 (tt) REVERT: H 166 GLU cc_start: 0.9335 (tp30) cc_final: 0.9079 (tp30) REVERT: H 173 GLN cc_start: 0.9360 (tm-30) cc_final: 0.9094 (tm-30) REVERT: I 41 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7892 (tm-30) REVERT: I 47 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7739 (mm-30) REVERT: I 165 PHE cc_start: 0.8782 (m-80) cc_final: 0.8443 (m-80) REVERT: J 52 ARG cc_start: 0.8826 (ptp90) cc_final: 0.8119 (mtm-85) REVERT: J 80 GLN cc_start: 0.9633 (OUTLIER) cc_final: 0.9312 (tp40) REVERT: K 80 GLN cc_start: 0.9560 (OUTLIER) cc_final: 0.9155 (tp40) REVERT: K 91 TYR cc_start: 0.8924 (t80) cc_final: 0.8599 (t80) REVERT: K 173 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8882 (tm-30) REVERT: L 14 GLN cc_start: 0.8870 (pt0) cc_final: 0.8567 (pt0) REVERT: L 47 GLU cc_start: 0.8486 (pm20) cc_final: 0.8280 (pm20) REVERT: L 89 LEU cc_start: 0.9674 (tp) cc_final: 0.9464 (tt) REVERT: L 173 GLN cc_start: 0.9672 (OUTLIER) cc_final: 0.9451 (tt0) REVERT: L 188 LYS cc_start: 0.9432 (mmmm) cc_final: 0.8757 (tppp) outliers start: 87 outliers final: 64 residues processed: 351 average time/residue: 0.3079 time to fit residues: 161.9224 Evaluate side-chains 337 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 266 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 195 GLN 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 18 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 86 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 36 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 220 SER Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 49 SER 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 47 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 194 HIS 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 212 PHE 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 83 PHE Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR 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 18 THR Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 80 GLN Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 173 GLN Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 194 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 161 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.065099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.052588 restraints weight = 84603.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.054026 restraints weight = 38598.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.055104 restraints weight = 23263.172| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.8480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19044 Z= 0.167 Angle : 0.646 15.137 25872 Z= 0.319 Chirality : 0.039 0.298 2952 Planarity : 0.004 0.038 3096 Dihedral : 4.171 38.344 2444 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.41 % Allowed : 22.65 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.18), residues: 2220 helix: 2.78 (0.12), residues: 1680 sheet: -1.78 (0.35), residues: 204 loop : -2.14 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 44 HIS 0.005 0.001 HIS E 194 PHE 0.020 0.001 PHE I 232 TYR 0.027 0.001 TYR F 65 ARG 0.008 0.001 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 1392) hydrogen bonds : angle 3.25100 ( 4176) SS BOND : bond 0.00312 ( 36) SS BOND : angle 0.99602 ( 72) covalent geometry : bond 0.00384 (19008) covalent geometry : angle 0.64498 (25800) *********************** 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 361 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 271 time to evaluate : 2.119 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: A 52 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7362 (mtm-85) REVERT: B 56 GLN cc_start: 0.9425 (mt0) cc_final: 0.8638 (mt0) REVERT: B 91 TYR cc_start: 0.8676 (t80) cc_final: 0.8306 (t80) REVERT: B 188 LYS cc_start: 0.9131 (mmmm) cc_final: 0.8896 (mmmm) REVERT: C 34 LEU cc_start: 0.9740 (tp) cc_final: 0.9276 (pp) REVERT: C 47 GLU cc_start: 0.8109 (pt0) cc_final: 0.7665 (mt-10) REVERT: C 160 LEU cc_start: 0.9672 (tp) cc_final: 0.9359 (pp) REVERT: C 188 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8910 (mmmm) REVERT: D 34 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9257 (pp) REVERT: D 188 LYS cc_start: 0.9246 (mmmm) cc_final: 0.8888 (mmmm) REVERT: E 56 GLN cc_start: 0.9472 (mt0) cc_final: 0.8672 (mt0) REVERT: E 65 TYR cc_start: 0.9442 (t80) cc_final: 0.8911 (t80) REVERT: E 173 GLN cc_start: 0.9616 (tm-30) cc_final: 0.8936 (tm-30) REVERT: F 56 GLN cc_start: 0.9292 (pt0) cc_final: 0.8979 (pt0) REVERT: F 91 TYR cc_start: 0.8618 (t80) cc_final: 0.8219 (t80) REVERT: F 173 GLN cc_start: 0.9605 (tm-30) cc_final: 0.8863 (tm-30) REVERT: F 195 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8862 (pt0) REVERT: F 205 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8711 (mt-10) REVERT: F 227 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8861 (mm-30) REVERT: G 47 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8029 (pm20) REVERT: G 56 GLN cc_start: 0.9552 (mm-40) cc_final: 0.9339 (mm-40) REVERT: H 41 GLU cc_start: 0.8842 (tp30) cc_final: 0.8625 (tm-30) REVERT: H 47 GLU cc_start: 0.8224 (pt0) cc_final: 0.8017 (pt0) REVERT: H 65 TYR cc_start: 0.9489 (t80) cc_final: 0.9246 (t80) REVERT: H 92 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9107 (tt) REVERT: H 166 GLU cc_start: 0.9335 (tp30) cc_final: 0.9086 (tp30) REVERT: H 173 GLN cc_start: 0.9352 (tm-30) cc_final: 0.9100 (tm-30) REVERT: I 41 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7977 (tm-30) REVERT: I 47 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7636 (mm-30) REVERT: K 91 TYR cc_start: 0.8957 (t80) cc_final: 0.8610 (t80) REVERT: K 173 GLN cc_start: 0.9265 (tm-30) cc_final: 0.8888 (tm-30) REVERT: L 14 GLN cc_start: 0.8874 (pt0) cc_final: 0.8578 (pt0) REVERT: L 34 LEU cc_start: 0.9710 (tp) cc_final: 0.9387 (pp) REVERT: L 89 LEU cc_start: 0.9676 (tp) cc_final: 0.9475 (tt) REVERT: L 99 MET cc_start: 0.8466 (tmm) cc_final: 0.8131 (tmm) REVERT: L 166 GLU cc_start: 0.9397 (tp30) cc_final: 0.9138 (tp30) REVERT: L 173 GLN cc_start: 0.9684 (OUTLIER) cc_final: 0.9460 (tt0) REVERT: L 188 LYS cc_start: 0.9441 (mmmm) cc_final: 0.8757 (tppp) outliers start: 90 outliers final: 72 residues processed: 337 average time/residue: 0.3060 time to fit residues: 153.1785 Evaluate side-chains 337 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 259 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 18 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 188 LYS 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 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 D residue 221 LEU Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 36 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 220 SER Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 171 LEU 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 86 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 212 PHE 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 83 PHE Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain J residue 16 TYR 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 218 LEU Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 16 TYR 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 86 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 173 GLN Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 194 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 207 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 198 optimal weight: 0.1980 chunk 89 optimal weight: 6.9990 chunk 37 optimal weight: 40.0000 chunk 179 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- 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 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.064797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.052337 restraints weight = 85185.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.053778 restraints weight = 38446.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.054858 restraints weight = 23099.895| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.8849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19044 Z= 0.156 Angle : 0.652 15.362 25872 Z= 0.321 Chirality : 0.039 0.236 2952 Planarity : 0.004 0.038 3096 Dihedral : 4.130 38.352 2444 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.02 % Allowed : 23.14 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.18), residues: 2220 helix: 2.75 (0.12), residues: 1680 sheet: -1.87 (0.34), residues: 204 loop : -2.05 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 44 HIS 0.004 0.001 HIS E 194 PHE 0.019 0.001 PHE I 232 TYR 0.024 0.001 TYR C 65 ARG 0.009 0.001 ARG D 52 Details of bonding type rmsd hydrogen bonds : bond 0.03082 ( 1392) hydrogen bonds : angle 3.28337 ( 4176) SS BOND : bond 0.00283 ( 36) SS BOND : angle 0.95866 ( 72) covalent geometry : bond 0.00358 (19008) covalent geometry : angle 0.65074 (25800) *********************** 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 355 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 273 time to evaluate : 2.144 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: A 52 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7559 (mtm-85) REVERT: A 61 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8523 (mm-30) REVERT: B 56 GLN cc_start: 0.9451 (mt0) cc_final: 0.8668 (mt0) REVERT: B 61 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8512 (mm-30) REVERT: B 91 TYR cc_start: 0.8712 (t80) cc_final: 0.8294 (t80) REVERT: B 166 GLU cc_start: 0.9402 (tp30) cc_final: 0.9085 (tp30) REVERT: B 188 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8910 (mmmm) REVERT: C 34 LEU cc_start: 0.9731 (tp) cc_final: 0.9269 (pp) REVERT: C 48 GLN cc_start: 0.9504 (tp40) cc_final: 0.8911 (tp40) REVERT: C 160 LEU cc_start: 0.9676 (tp) cc_final: 0.9371 (pp) REVERT: C 188 LYS cc_start: 0.9181 (mmmm) cc_final: 0.8550 (tppp) REVERT: D 34 LEU cc_start: 0.9697 (tp) cc_final: 0.9297 (pp) REVERT: D 188 LYS cc_start: 0.9260 (mmmm) cc_final: 0.8896 (mmmm) REVERT: E 56 GLN cc_start: 0.9494 (mt0) cc_final: 0.8484 (mt0) REVERT: E 61 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8360 (mm-30) REVERT: E 173 GLN cc_start: 0.9621 (tm-30) cc_final: 0.8917 (tm-30) REVERT: F 52 ARG cc_start: 0.7996 (mtm110) cc_final: 0.7773 (mtm110) REVERT: F 56 GLN cc_start: 0.9307 (pt0) cc_final: 0.9066 (pt0) REVERT: F 91 TYR cc_start: 0.8718 (t80) cc_final: 0.8282 (t80) REVERT: F 173 GLN cc_start: 0.9618 (tm-30) cc_final: 0.8867 (tm-30) REVERT: F 205 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8665 (mt-10) REVERT: G 34 LEU cc_start: 0.9715 (tp) cc_final: 0.9412 (pp) REVERT: G 41 GLU cc_start: 0.8490 (pm20) cc_final: 0.8228 (pm20) REVERT: G 47 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: G 56 GLN cc_start: 0.9560 (mm-40) cc_final: 0.9345 (mm-40) REVERT: H 92 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9130 (tt) REVERT: H 166 GLU cc_start: 0.9316 (tp30) cc_final: 0.9065 (tp30) REVERT: H 173 GLN cc_start: 0.9351 (tm-30) cc_final: 0.9103 (tm-30) REVERT: I 41 GLU cc_start: 0.8228 (tm-30) cc_final: 0.8014 (tm-30) REVERT: I 47 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7603 (mm-30) REVERT: K 91 TYR cc_start: 0.8976 (t80) cc_final: 0.8606 (t80) REVERT: K 223 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9433 (mp) REVERT: L 14 GLN cc_start: 0.8854 (pt0) cc_final: 0.8575 (pt0) REVERT: L 34 LEU cc_start: 0.9720 (tp) cc_final: 0.9414 (pp) REVERT: L 47 GLU cc_start: 0.8559 (pm20) cc_final: 0.7831 (mp0) REVERT: L 99 MET cc_start: 0.8482 (tmm) cc_final: 0.8199 (tmm) REVERT: L 166 GLU cc_start: 0.9379 (tp30) cc_final: 0.9135 (tp30) REVERT: L 173 GLN cc_start: 0.9677 (OUTLIER) cc_final: 0.9448 (tt0) REVERT: L 188 LYS cc_start: 0.9451 (mmmm) cc_final: 0.8766 (tppp) outliers start: 82 outliers final: 70 residues processed: 337 average time/residue: 0.3174 time to fit residues: 159.6116 Evaluate side-chains 340 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 266 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 18 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 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 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 31 PHE Chi-restraints excluded: chain E residue 36 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 220 SER 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 49 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 171 LEU 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 49 SER 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 55 THR Chi-restraints excluded: chain I residue 83 PHE Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain J residue 16 TYR 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 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 68 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 88 THR 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 86 VAL Chi-restraints excluded: chain L residue 173 GLN Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 194 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 53 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 161 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 109 optimal weight: 40.0000 chunk 112 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.065024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.052529 restraints weight = 84226.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.054006 restraints weight = 38130.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.055015 restraints weight = 23106.871| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.9024 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= 0.141 Angle : 0.675 15.402 25872 Z= 0.327 Chirality : 0.039 0.307 2952 Planarity : 0.004 0.039 3096 Dihedral : 4.092 38.856 2442 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.68 % Allowed : 23.82 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.18), residues: 2220 helix: 2.74 (0.12), residues: 1680 sheet: -1.87 (0.34), residues: 204 loop : -2.00 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 44 HIS 0.007 0.001 HIS E 194 PHE 0.022 0.001 PHE J 165 TYR 0.025 0.001 TYR H 65 ARG 0.008 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 1392) hydrogen bonds : angle 3.28178 ( 4176) SS BOND : bond 0.00288 ( 36) SS BOND : angle 0.92853 ( 72) covalent geometry : bond 0.00327 (19008) covalent geometry : angle 0.67382 (25800) ********************** 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 348 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 273 time to evaluate : 1.988 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: 0.8392 (p0) cc_final: 0.7807 (p0) REVERT: A 52 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7584 (mtm-85) REVERT: B 56 GLN cc_start: 0.9434 (mt0) cc_final: 0.8649 (mt0) REVERT: B 91 TYR cc_start: 0.8720 (t80) cc_final: 0.8290 (t80) REVERT: B 166 GLU cc_start: 0.9409 (tp30) cc_final: 0.9079 (tp30) REVERT: B 188 LYS cc_start: 0.9162 (mmmm) cc_final: 0.8899 (mmmm) REVERT: C 34 LEU cc_start: 0.9723 (tp) cc_final: 0.9274 (pp) REVERT: C 47 GLU cc_start: 0.8113 (pt0) cc_final: 0.7842 (mt-10) REVERT: C 48 GLN cc_start: 0.9494 (tp40) cc_final: 0.8957 (tp40) REVERT: C 160 LEU cc_start: 0.9672 (tp) cc_final: 0.9374 (pp) REVERT: C 188 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8498 (tppp) REVERT: D 34 LEU cc_start: 0.9696 (tp) cc_final: 0.9271 (pp) REVERT: D 56 GLN cc_start: 0.9534 (mt0) cc_final: 0.8523 (mt0) REVERT: D 188 LYS cc_start: 0.9260 (mmmm) cc_final: 0.8886 (mmmm) REVERT: E 56 GLN cc_start: 0.9476 (mt0) cc_final: 0.8683 (mt0) REVERT: E 61 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8287 (mm-30) REVERT: E 173 GLN cc_start: 0.9621 (tm-30) cc_final: 0.8908 (tm-30) REVERT: F 52 ARG cc_start: 0.8022 (mtm110) cc_final: 0.7766 (mtm110) REVERT: F 56 GLN cc_start: 0.9287 (pt0) cc_final: 0.9039 (pt0) REVERT: F 91 TYR cc_start: 0.8780 (t80) cc_final: 0.8321 (t80) REVERT: F 173 GLN cc_start: 0.9610 (tm-30) cc_final: 0.8851 (tm-30) REVERT: F 205 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8680 (mt-10) REVERT: G 34 LEU cc_start: 0.9721 (tp) cc_final: 0.9414 (pp) REVERT: G 41 GLU cc_start: 0.8503 (pm20) cc_final: 0.8268 (pm20) REVERT: G 56 GLN cc_start: 0.9545 (mm-40) cc_final: 0.9319 (mt0) REVERT: H 89 LEU cc_start: 0.9490 (tt) cc_final: 0.9287 (mm) REVERT: H 92 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9130 (tt) REVERT: H 166 GLU cc_start: 0.9336 (tp30) cc_final: 0.9091 (tp30) REVERT: H 173 GLN cc_start: 0.9345 (tm-30) cc_final: 0.9116 (tm-30) REVERT: I 41 GLU cc_start: 0.8273 (tm-30) cc_final: 0.8040 (tm-30) REVERT: I 56 GLN cc_start: 0.9538 (mt0) cc_final: 0.9046 (mt0) REVERT: J 188 LYS cc_start: 0.9225 (tppt) cc_final: 0.8986 (mmmm) REVERT: K 91 TYR cc_start: 0.8961 (t80) cc_final: 0.8571 (t80) REVERT: L 14 GLN cc_start: 0.8876 (pt0) cc_final: 0.8617 (pt0) REVERT: L 34 LEU cc_start: 0.9722 (tp) cc_final: 0.9431 (pp) REVERT: L 47 GLU cc_start: 0.8550 (pm20) cc_final: 0.7785 (mp0) REVERT: L 99 MET cc_start: 0.8479 (tmm) cc_final: 0.8229 (tmm) REVERT: L 166 GLU cc_start: 0.9418 (tp30) cc_final: 0.9187 (tp30) REVERT: L 173 GLN cc_start: 0.9675 (OUTLIER) cc_final: 0.9443 (tt0) REVERT: L 188 LYS cc_start: 0.9452 (mmmm) cc_final: 0.9229 (mmmm) REVERT: L 205 GLU cc_start: 0.9336 (tp30) cc_final: 0.8971 (mm-30) outliers start: 75 outliers final: 67 residues processed: 332 average time/residue: 0.3006 time to fit residues: 148.7848 Evaluate side-chains 334 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 264 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 229 PHE 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 188 LYS 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 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 31 PHE Chi-restraints excluded: chain E residue 36 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 220 SER 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 49 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 171 LEU 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 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 55 THR Chi-restraints excluded: chain I residue 83 PHE Chi-restraints excluded: chain I residue 86 VAL Chi-restraints excluded: chain J residue 16 TYR 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 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 68 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 173 GLN Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 194 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 43 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 146 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.065173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.052769 restraints weight = 84578.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.054247 restraints weight = 37787.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.055298 restraints weight = 22766.011| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.9180 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= 0.133 Angle : 0.668 15.260 25872 Z= 0.324 Chirality : 0.039 0.375 2952 Planarity : 0.004 0.039 3096 Dihedral : 4.073 39.054 2442 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.48 % Allowed : 23.92 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.18), residues: 2220 helix: 2.71 (0.12), residues: 1680 sheet: -1.85 (0.35), residues: 204 loop : -1.96 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 44 HIS 0.004 0.001 HIS E 194 PHE 0.026 0.001 PHE J 165 TYR 0.029 0.001 TYR H 65 ARG 0.009 0.000 ARG D 52 Details of bonding type rmsd hydrogen bonds : bond 0.03008 ( 1392) hydrogen bonds : angle 3.27456 ( 4176) SS BOND : bond 0.00274 ( 36) SS BOND : angle 0.89312 ( 72) covalent geometry : bond 0.00307 (19008) covalent geometry : angle 0.66704 (25800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5484.01 seconds wall clock time: 98 minutes 6.10 seconds (5886.10 seconds total)