Starting phenix.real_space_refine on Mon Jun 16 07:36:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qko_18468/06_2025/8qko_18468_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qko_18468/06_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_18468/06_2025/8qko_18468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qko_18468/06_2025/8qko_18468.map" model { file = "/net/cci-nas-00/data/ceres_data/8qko_18468/06_2025/8qko_18468_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qko_18468/06_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-5710/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: 11.98, per 1000 atoms: 0.65 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: 5.14 Conformation dependent library (CDL) restraints added in 2.5 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: 1.64 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: 6.21 Time building geometry restraints manager: 5.93 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: 0.17 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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 43.990 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.240 ------------------------------------------------------------------------------- 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 : 1.922 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: 0.3073 time to fit residues: 284.1768 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 : 1.960 ------------------------------------------------------------------------------- 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 = 0.076158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.063158 restraints weight = 81154.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.064883 restraints weight = 41093.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.066052 restraints weight = 25523.553| |-----------------------------------------------------------------------------| 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 10.844 25872 Z= 0.325 Chirality : 0.040 0.226 2952 Planarity : 0.004 0.051 3096 Dihedral : 5.271 49.319 2483 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.13 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 3.34664 ( 4176) SS BOND : bond 0.00504 ( 36) SS BOND : angle 1.83438 ( 72) covalent geometry : bond 0.00381 (19008) covalent geometry : angle 0.64637 (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 : 2.338 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: 0.8727 (mt0) REVERT: A 61 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8341 (mm-30) REVERT: A 91 TYR cc_start: 0.8602 (t80) cc_final: 0.8359 (t80) REVERT: B 48 GLN cc_start: 0.9560 (OUTLIER) cc_final: 0.9048 (tp40) REVERT: B 61 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7884 (mm-30) REVERT: B 65 TYR cc_start: 0.9227 (t80) cc_final: 0.8972 (t80) REVERT: B 91 TYR cc_start: 0.8447 (t80) cc_final: 0.8206 (t80) REVERT: C 46 ASP cc_start: 0.7242 (p0) cc_final: 0.6949 (p0) REVERT: C 61 GLU cc_start: 0.7816 (mp0) cc_final: 0.7495 (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: 0.5096 (OUTLIER) cc_final: 0.3882 (p) REVERT: D 164 ILE cc_start: 0.8945 (mm) cc_final: 0.8527 (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: 0.7170 (tp30) REVERT: E 56 GLN cc_start: 0.9413 (mt0) cc_final: 0.9060 (mt0) REVERT: F 52 ARG cc_start: 0.7492 (mtm-85) cc_final: 0.7078 (mtm-85) REVERT: F 56 GLN cc_start: 0.8475 (pt0) cc_final: 0.7911 (pt0) REVERT: F 173 GLN cc_start: 0.9385 (tm-30) cc_final: 0.8876 (tm-30) REVERT: F 227 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8236 (mm-30) REVERT: G 25 LEU cc_start: 0.9493 (mt) cc_final: 0.9206 (pp) REVERT: G 63 VAL cc_start: 0.9283 (m) cc_final: 0.9072 (p) REVERT: H 41 GLU cc_start: 0.8575 (tp30) cc_final: 0.8193 (tm-30) REVERT: H 99 MET cc_start: 0.8899 (mmp) cc_final: 0.8366 (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: 0.8744 (tm-30) REVERT: H 205 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7639 (mp0) REVERT: I 188 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8741 (mmmm) REVERT: J 56 GLN cc_start: 0.8700 (mt0) cc_final: 0.8404 (mt0) REVERT: J 212 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8491 (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: 0.8752 (ttmm) REVERT: L 80 GLN cc_start: 0.8835 (tt0) cc_final: 0.8301 (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: 0.3043 time to fit residues: 197.2445 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 : 2.357 ------------------------------------------------------------------------------- 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: 9.9990 chunk 124 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 5 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- 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** F 48 GLN K 194 HIS L 57 GLN ** L 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.071998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.059421 restraints weight = 80607.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.061109 restraints weight = 39432.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.062183 restraints weight = 24044.476| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5125 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= 0.194 Angle : 0.645 11.930 25872 Z= 0.329 Chirality : 0.040 0.228 2952 Planarity : 0.004 0.063 3096 Dihedral : 4.836 58.060 2457 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.51 % Allowed : 16.57 % 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: 2.22 (0.17), residues: 2220 helix: 2.54 (0.11), residues: 1668 sheet: -1.73 (0.33), residues: 204 loop : -2.00 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 44 HIS 0.007 0.001 HIS H 194 PHE 0.034 0.001 PHE C 212 TYR 0.023 0.001 TYR E 91 ARG 0.005 0.001 ARG F 202 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 1392) hydrogen bonds : angle 3.30844 ( 4176) SS BOND : bond 0.00434 ( 36) SS BOND : angle 1.60951 ( 72) covalent geometry : bond 0.00402 (19008) covalent geometry : angle 0.63989 (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 431 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 339 time to evaluate : 2.129 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: A 46 ASP cc_start: 0.8531 (p0) cc_final: 0.7930 (p0) REVERT: A 61 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8425 (tp30) REVERT: A 91 TYR cc_start: 0.8691 (t80) cc_final: 0.8302 (t80) REVERT: B 46 ASP cc_start: 0.8568 (p0) cc_final: 0.8063 (p0) REVERT: B 56 GLN cc_start: 0.9404 (mt0) cc_final: 0.8763 (mt0) REVERT: C 38 THR cc_start: 0.8735 (t) cc_final: 0.8491 (t) REVERT: C 47 GLU cc_start: 0.7941 (pt0) cc_final: 0.7701 (pt0) REVERT: C 179 PHE cc_start: 0.8090 (m-80) cc_final: 0.7625 (m-80) REVERT: D 41 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7970 (mt-10) REVERT: D 47 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7124 (mt-10) REVERT: E 47 GLU cc_start: 0.8822 (tp30) cc_final: 0.8295 (tp30) REVERT: E 56 GLN cc_start: 0.9503 (mt0) cc_final: 0.9135 (mt0) REVERT: E 65 TYR cc_start: 0.8710 (t80) cc_final: 0.8339 (t80) REVERT: F 56 GLN cc_start: 0.8859 (pt0) cc_final: 0.8356 (pt0) REVERT: F 71 ILE cc_start: 0.9438 (pt) cc_final: 0.9225 (tp) REVERT: F 195 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8789 (mp10) REVERT: F 205 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8395 (mt-10) REVERT: F 227 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8458 (mm-30) REVERT: G 32 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8562 (ptp-110) REVERT: G 41 GLU cc_start: 0.8427 (pp20) cc_final: 0.8216 (pp20) REVERT: G 52 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.8457 (mmm-85) REVERT: G 66 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8755 (m-30) REVERT: G 165 PHE cc_start: 0.8122 (m-80) cc_final: 0.7823 (m-80) REVERT: H 8 LYS cc_start: 0.9659 (pttp) cc_final: 0.9389 (ptpp) REVERT: H 41 GLU cc_start: 0.8709 (tp30) cc_final: 0.8399 (tm-30) REVERT: H 61 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8470 (mm-30) REVERT: H 166 GLU cc_start: 0.9301 (tp30) cc_final: 0.8994 (tp30) REVERT: H 173 GLN cc_start: 0.9215 (tm-30) cc_final: 0.8911 (tm-30) REVERT: I 58 PRO cc_start: 0.8922 (Cg_exo) cc_final: 0.8688 (Cg_endo) REVERT: I 75 ARG cc_start: 0.9068 (mpp80) cc_final: 0.8159 (mmt90) REVERT: I 188 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8890 (mmmm) REVERT: J 52 ARG cc_start: 0.8742 (ptp90) cc_final: 0.8358 (mpp80) REVERT: J 56 GLN cc_start: 0.8910 (mt0) cc_final: 0.8262 (mt0) REVERT: J 75 ARG cc_start: 0.9111 (mpp80) cc_final: 0.8416 (mtt-85) REVERT: K 14 GLN cc_start: 0.8488 (pt0) cc_final: 0.7930 (pt0) REVERT: K 162 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8209 (mttp) REVERT: K 173 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8902 (tm-30) REVERT: K 205 GLU cc_start: 0.9203 (tp30) cc_final: 0.8927 (tp30) REVERT: L 48 GLN cc_start: 0.8156 (pm20) cc_final: 0.7455 (tt0) REVERT: L 218 LEU cc_start: 0.9641 (mm) cc_final: 0.9422 (mm) outliers start: 92 outliers final: 55 residues processed: 402 average time/residue: 0.2962 time to fit residues: 180.7226 Evaluate side-chains 349 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 291 time to evaluate : 2.079 ------------------------------------------------------------------------------- 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 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 55 THR Chi-restraints excluded: chain G residue 66 ASP 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 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 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 78 VAL Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 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: 9.9990 chunk 193 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 55 optimal weight: 50.0000 chunk 39 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN F 54 ASN ** G 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 ASN ** H 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 ASN K 48 GLN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN ** L 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 173 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.052653 restraints weight = 86107.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.054154 restraints weight = 40224.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.055152 restraints weight = 24398.111| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.7971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.152 19044 Z= 0.290 Angle : 0.736 15.626 25872 Z= 0.387 Chirality : 0.043 0.227 2952 Planarity : 0.005 0.059 3096 Dihedral : 5.246 56.390 2450 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 6.18 % Allowed : 18.24 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.65 (0.17), residues: 2220 helix: 2.18 (0.11), residues: 1668 sheet: -2.17 (0.33), residues: 204 loop : -2.28 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 77 HIS 0.013 0.002 HIS A 194 PHE 0.037 0.002 PHE G 165 TYR 0.029 0.002 TYR D 65 ARG 0.006 0.001 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 1392) hydrogen bonds : angle 3.76880 ( 4176) SS BOND : bond 0.00446 ( 36) SS BOND : angle 1.46142 ( 72) covalent geometry : bond 0.00649 (19008) covalent geometry : angle 0.73271 (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 399 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 273 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7738 (mtm110) cc_final: 0.7472 (mtm-85) REVERT: A 61 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8184 (tp30) REVERT: A 166 GLU cc_start: 0.9428 (tp30) cc_final: 0.9195 (tp30) REVERT: B 91 TYR cc_start: 0.8713 (t80) cc_final: 0.8283 (t80) REVERT: B 166 GLU cc_start: 0.9401 (tp30) cc_final: 0.9189 (tp30) REVERT: C 91 TYR cc_start: 0.8381 (t80) cc_final: 0.8161 (t80) REVERT: C 160 LEU cc_start: 0.9662 (tp) cc_final: 0.9384 (tt) REVERT: C 188 LYS cc_start: 0.9175 (mmmm) cc_final: 0.8884 (mmmm) REVERT: D 56 GLN cc_start: 0.9590 (mt0) cc_final: 0.9257 (mt0) REVERT: D 65 TYR cc_start: 0.9346 (OUTLIER) cc_final: 0.9141 (t80) REVERT: D 91 TYR cc_start: 0.8060 (t80) cc_final: 0.7790 (t80) REVERT: E 47 GLU cc_start: 0.8693 (tp30) cc_final: 0.8482 (tp30) REVERT: E 195 GLN cc_start: 0.8741 (pm20) cc_final: 0.8453 (pp30) REVERT: F 52 ARG cc_start: 0.8089 (mtm110) cc_final: 0.7565 (mtm110) REVERT: F 56 GLN cc_start: 0.9432 (pt0) cc_final: 0.8947 (pt0) REVERT: F 195 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.8944 (pt0) REVERT: F 196 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8795 (m) REVERT: F 227 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8768 (mm-30) REVERT: G 16 TYR cc_start: 0.6668 (OUTLIER) cc_final: 0.6424 (m-10) REVERT: G 47 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7997 (pm20) REVERT: H 8 LYS cc_start: 0.9681 (pttp) cc_final: 0.9425 (ptpp) REVERT: H 61 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8288 (tp30) REVERT: H 92 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9067 (tt) REVERT: H 166 GLU cc_start: 0.9377 (tp30) cc_final: 0.9095 (tp30) REVERT: H 173 GLN cc_start: 0.9434 (tm-30) cc_final: 0.9231 (tm-30) REVERT: I 188 LYS cc_start: 0.9412 (mmmm) cc_final: 0.9036 (mmmm) REVERT: J 56 GLN cc_start: 0.9395 (mt0) cc_final: 0.8743 (mt0) REVERT: J 227 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8976 (mm-30) REVERT: K 14 GLN cc_start: 0.8459 (pt0) cc_final: 0.8060 (pt0) REVERT: K 41 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8762 (tm-30) REVERT: K 91 TYR cc_start: 0.8876 (t80) cc_final: 0.8580 (t80) REVERT: K 166 GLU cc_start: 0.9366 (tp30) cc_final: 0.9152 (tp30) REVERT: K 173 GLN cc_start: 0.9252 (tm-30) cc_final: 0.9013 (tm-30) REVERT: L 89 LEU cc_start: 0.9685 (tp) cc_final: 0.9465 (tt) REVERT: L 166 GLU cc_start: 0.9413 (tp30) cc_final: 0.9131 (tp30) REVERT: L 188 LYS cc_start: 0.9423 (mmmm) cc_final: 0.8864 (tppp) outliers start: 126 outliers final: 66 residues processed: 368 average time/residue: 0.3104 time to fit residues: 171.4355 Evaluate side-chains 315 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 243 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 194 HIS 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 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 34 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 16 TYR Chi-restraints excluded: chain E residue 31 PHE 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 181 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 16 TYR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 47 GLU 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 154 THR Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 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 221 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 90 LEU Chi-restraints excluded: chain J residue 92 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 35 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 190 ASP 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: 5.9990 chunk 131 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 F 224 ASN H 194 HIS ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.064572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.052011 restraints weight = 86038.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.053435 restraints weight = 39508.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.054526 restraints weight = 23955.574| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.8469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19044 Z= 0.210 Angle : 0.632 12.556 25872 Z= 0.322 Chirality : 0.039 0.308 2952 Planarity : 0.004 0.036 3096 Dihedral : 4.643 52.701 2446 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.10 % Allowed : 21.03 % Favored : 73.87 % 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: 2.20 (0.17), residues: 2220 helix: 2.63 (0.11), residues: 1656 sheet: -2.07 (0.33), residues: 204 loop : -2.21 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 24 HIS 0.006 0.001 HIS G 73 PHE 0.033 0.001 PHE L 31 TYR 0.018 0.001 TYR F 65 ARG 0.005 0.001 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 1392) hydrogen bonds : angle 3.45972 ( 4176) SS BOND : bond 0.00436 ( 36) SS BOND : angle 1.28795 ( 72) covalent geometry : bond 0.00473 (19008) covalent geometry : angle 0.62895 (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 368 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 264 time to evaluate : 2.824 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: 0.8497 (p0) cc_final: 0.7992 (p0) REVERT: A 52 ARG cc_start: 0.7865 (mtm110) cc_final: 0.7472 (mtm-85) REVERT: A 166 GLU cc_start: 0.9326 (tp30) cc_final: 0.9054 (tp30) REVERT: B 52 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7736 (mpp-170) REVERT: B 91 TYR cc_start: 0.8800 (t80) cc_final: 0.8296 (t80) REVERT: B 166 GLU cc_start: 0.9317 (tp30) cc_final: 0.8964 (tp30) REVERT: C 91 TYR cc_start: 0.8519 (t80) cc_final: 0.8230 (t80) REVERT: C 160 LEU cc_start: 0.9687 (tp) cc_final: 0.9351 (pp) REVERT: D 34 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9426 (pp) REVERT: D 56 GLN cc_start: 0.9572 (mt0) cc_final: 0.9033 (mt0) REVERT: D 188 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8925 (mmmm) REVERT: E 46 ASP cc_start: 0.9040 (p0) cc_final: 0.8798 (p0) REVERT: E 56 GLN cc_start: 0.9484 (mt0) cc_final: 0.9192 (mt0) REVERT: E 91 TYR cc_start: 0.7825 (t80) cc_final: 0.7609 (t80) REVERT: F 52 ARG cc_start: 0.8204 (mtm110) cc_final: 0.7495 (mtm110) REVERT: F 56 GLN cc_start: 0.9442 (pt0) cc_final: 0.9212 (pt0) REVERT: F 166 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8880 (tm-30) REVERT: F 173 GLN cc_start: 0.9558 (tm-30) cc_final: 0.8957 (tm-30) REVERT: F 195 GLN cc_start: 0.9247 (pm20) cc_final: 0.8927 (pt0) REVERT: F 227 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8795 (mm-30) REVERT: G 47 GLU cc_start: 0.8211 (mp0) cc_final: 0.7935 (mp0) REVERT: G 61 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8081 (tm-30) REVERT: H 166 GLU cc_start: 0.9336 (tp30) cc_final: 0.9099 (tp30) REVERT: H 173 GLN cc_start: 0.9391 (tm-30) cc_final: 0.9180 (tm-30) REVERT: I 38 THR cc_start: 0.9329 (p) cc_final: 0.9115 (p) REVERT: I 41 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7930 (pp20) REVERT: I 52 ARG cc_start: 0.8780 (ptp90) cc_final: 0.7977 (mtm-85) REVERT: I 188 LYS cc_start: 0.9359 (mmmm) cc_final: 0.9030 (mmmm) REVERT: J 227 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8972 (mm-30) REVERT: K 91 TYR cc_start: 0.8954 (t80) cc_final: 0.8640 (t80) REVERT: K 166 GLU cc_start: 0.9369 (tp30) cc_final: 0.9122 (tp30) REVERT: K 173 GLN cc_start: 0.9348 (tm-30) cc_final: 0.8958 (tm-30) REVERT: K 223 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9417 (mp) REVERT: L 89 LEU cc_start: 0.9692 (tp) cc_final: 0.9467 (tt) REVERT: L 166 GLU cc_start: 0.9442 (tp30) cc_final: 0.9199 (tp30) REVERT: L 188 LYS cc_start: 0.9428 (mmmm) cc_final: 0.8777 (tppp) outliers start: 104 outliers final: 69 residues processed: 345 average time/residue: 0.3495 time to fit residues: 180.8992 Evaluate side-chains 307 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 236 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain D residue 16 TYR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain 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 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 90 LEU Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 32 ARG 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 154 THR Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 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 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 86 VAL 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 212 PHE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 85 SER 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 23 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 190 ASP 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: 20.0000 chunk 31 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 73 optimal weight: 40.0000 chunk 132 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** E 57 GLN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 GLN J 195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.063920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.051453 restraints weight = 86916.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.052886 restraints weight = 39333.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.053866 restraints weight = 23751.904| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.8859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19044 Z= 0.190 Angle : 0.633 11.159 25872 Z= 0.320 Chirality : 0.039 0.330 2952 Planarity : 0.004 0.040 3096 Dihedral : 4.575 48.760 2446 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.95 % Allowed : 21.32 % Favored : 73.73 % 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: 2.31 (0.18), residues: 2220 helix: 2.70 (0.11), residues: 1668 sheet: -2.06 (0.34), residues: 204 loop : -2.23 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP K 77 HIS 0.005 0.001 HIS D 73 PHE 0.024 0.001 PHE L 31 TYR 0.016 0.001 TYR K 65 ARG 0.007 0.001 ARG D 52 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 1392) hydrogen bonds : angle 3.37718 ( 4176) SS BOND : bond 0.00384 ( 36) SS BOND : angle 1.10854 ( 72) covalent geometry : bond 0.00433 (19008) covalent geometry : angle 0.63145 (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 364 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 263 time to evaluate : 2.197 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: 0.7886 (mtm110) cc_final: 0.7411 (mpp-170) REVERT: B 61 GLU cc_start: 0.8839 (tp30) cc_final: 0.8604 (mm-30) REVERT: B 188 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8872 (mmmm) REVERT: C 56 GLN cc_start: 0.9656 (mt0) cc_final: 0.9089 (mt0) REVERT: C 61 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8408 (mm-30) REVERT: C 91 TYR cc_start: 0.8677 (t80) cc_final: 0.8302 (t80) REVERT: C 160 LEU cc_start: 0.9701 (tp) cc_final: 0.9406 (pp) REVERT: C 188 LYS cc_start: 0.9225 (mmmm) cc_final: 0.8645 (tppp) REVERT: D 34 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9401 (pp) REVERT: D 188 LYS cc_start: 0.9251 (mmmm) cc_final: 0.8884 (mmmm) REVERT: E 61 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8299 (mm-30) REVERT: E 173 GLN cc_start: 0.9625 (tm-30) cc_final: 0.8939 (tm-30) REVERT: F 52 ARG cc_start: 0.8137 (mtm110) cc_final: 0.7476 (mtm110) REVERT: F 56 GLN cc_start: 0.9405 (pt0) cc_final: 0.9186 (pt0) REVERT: F 173 GLN cc_start: 0.9556 (tm-30) cc_final: 0.8911 (tm-30) REVERT: F 195 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.9068 (mt0) REVERT: H 166 GLU cc_start: 0.9333 (tp30) cc_final: 0.9081 (tp30) REVERT: H 173 GLN cc_start: 0.9387 (tm-30) cc_final: 0.9164 (tm-30) REVERT: I 188 LYS cc_start: 0.9351 (mmmm) cc_final: 0.8981 (mmmm) REVERT: J 205 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8772 (mm-30) REVERT: J 227 GLU cc_start: 0.9239 (mm-30) cc_final: 0.9002 (mm-30) REVERT: K 14 GLN cc_start: 0.8526 (pt0) cc_final: 0.8230 (pt0) REVERT: K 91 TYR cc_start: 0.8990 (t80) cc_final: 0.8602 (t80) REVERT: K 173 GLN cc_start: 0.9287 (tm-30) cc_final: 0.8927 (tm-30) REVERT: K 223 LEU cc_start: 0.9673 (OUTLIER) cc_final: 0.9432 (mp) REVERT: L 34 LEU cc_start: 0.9737 (tp) cc_final: 0.9428 (pp) REVERT: L 89 LEU cc_start: 0.9692 (tp) cc_final: 0.9472 (tt) REVERT: L 166 GLU cc_start: 0.9461 (tp30) cc_final: 0.9201 (tp30) REVERT: L 188 LYS cc_start: 0.9432 (mmmm) cc_final: 0.8741 (tppp) outliers start: 101 outliers final: 75 residues processed: 340 average time/residue: 0.3192 time to fit residues: 162.1542 Evaluate side-chains 321 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 243 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain D residue 16 TYR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 34 LEU 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 229 PHE Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU 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 32 ARG 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 154 THR Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 78 VAL 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 J residue 16 TYR Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain J residue 55 THR 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 68 SER Chi-restraints excluded: chain K residue 78 VAL 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 K residue 229 PHE Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 135 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 19 optimal weight: 40.0000 chunk 105 optimal weight: 2.9990 chunk 109 optimal weight: 40.0000 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN F 54 ASN G 224 ASN H 54 ASN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.063942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.051737 restraints weight = 84868.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.053158 restraints weight = 38707.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.054140 restraints weight = 23274.045| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.9007 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 : 0.620 12.844 25872 Z= 0.306 Chirality : 0.038 0.312 2952 Planarity : 0.004 0.040 3096 Dihedral : 4.453 52.227 2446 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.17 % Allowed : 22.65 % Favored : 73.19 % 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: 2.42 (0.18), residues: 2220 helix: 2.79 (0.12), residues: 1668 sheet: -1.98 (0.34), residues: 204 loop : -2.27 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP K 77 HIS 0.005 0.001 HIS G 73 PHE 0.024 0.001 PHE L 31 TYR 0.013 0.001 TYR E 65 ARG 0.008 0.000 ARG B 100 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 1392) hydrogen bonds : angle 3.28467 ( 4176) SS BOND : bond 0.00294 ( 36) SS BOND : angle 0.97165 ( 72) covalent geometry : bond 0.00307 (19008) covalent geometry : angle 0.61917 (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 359 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 274 time to evaluate : 2.135 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: 0.7900 (mtm110) cc_final: 0.7436 (mpp-170) REVERT: A 173 GLN cc_start: 0.9525 (tm-30) cc_final: 0.9219 (tm-30) REVERT: B 52 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7455 (mtm-85) REVERT: B 56 GLN cc_start: 0.9446 (mt0) cc_final: 0.8755 (mt0) REVERT: B 173 GLN cc_start: 0.9542 (tm-30) cc_final: 0.9238 (tm-30) REVERT: B 188 LYS cc_start: 0.9122 (mmmm) cc_final: 0.8820 (mmmm) REVERT: B 195 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7875 (pp30) REVERT: C 56 GLN cc_start: 0.9635 (mt0) cc_final: 0.8825 (mt0) REVERT: C 91 TYR cc_start: 0.8742 (t80) cc_final: 0.8312 (t80) REVERT: C 160 LEU cc_start: 0.9697 (tp) cc_final: 0.9403 (pp) REVERT: C 188 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8557 (tppp) REVERT: D 34 LEU cc_start: 0.9690 (OUTLIER) cc_final: 0.9390 (pp) REVERT: D 188 LYS cc_start: 0.9259 (mmmm) cc_final: 0.8856 (mmmm) REVERT: E 56 GLN cc_start: 0.9430 (mt0) cc_final: 0.8310 (mt0) REVERT: E 173 GLN cc_start: 0.9588 (tm-30) cc_final: 0.8915 (tm-30) REVERT: F 56 GLN cc_start: 0.9323 (pt0) cc_final: 0.9087 (pt0) REVERT: F 173 GLN cc_start: 0.9541 (tm-30) cc_final: 0.8893 (tm-30) REVERT: F 195 GLN cc_start: 0.9226 (pm20) cc_final: 0.8936 (pt0) REVERT: F 196 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8667 (m) REVERT: G 41 GLU cc_start: 0.8414 (pm20) cc_final: 0.8188 (pm20) REVERT: G 61 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7972 (tm-30) REVERT: H 38 THR cc_start: 0.9276 (m) cc_final: 0.9071 (t) REVERT: H 166 GLU cc_start: 0.9321 (tp30) cc_final: 0.9070 (tp30) REVERT: H 173 GLN cc_start: 0.9359 (tm-30) cc_final: 0.9136 (tm-30) REVERT: I 188 LYS cc_start: 0.9335 (mmmm) cc_final: 0.8939 (mmmm) REVERT: J 227 GLU cc_start: 0.9239 (mm-30) cc_final: 0.9020 (mm-30) REVERT: K 91 TYR cc_start: 0.8982 (t80) cc_final: 0.8551 (t80) REVERT: K 223 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9416 (mp) REVERT: L 34 LEU cc_start: 0.9730 (tp) cc_final: 0.9428 (pp) REVERT: L 166 GLU cc_start: 0.9462 (tp30) cc_final: 0.9156 (tp30) REVERT: L 188 LYS cc_start: 0.9433 (mmmm) cc_final: 0.8732 (tppp) outliers start: 85 outliers final: 70 residues processed: 341 average time/residue: 0.3174 time to fit residues: 161.0783 Evaluate side-chains 328 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 254 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 86 VAL 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 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 89 LEU Chi-restraints excluded: chain D residue 154 THR 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 34 LEU 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 196 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 49 SER 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 54 ASN 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 55 THR Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 86 VAL 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 18 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 161 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.064192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.052028 restraints weight = 85095.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.053454 restraints weight = 38603.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.054415 restraints weight = 23372.053| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.9137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19044 Z= 0.121 Angle : 0.630 11.687 25872 Z= 0.309 Chirality : 0.038 0.259 2952 Planarity : 0.004 0.041 3096 Dihedral : 4.416 59.347 2446 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.31 % Allowed : 22.79 % Favored : 72.89 % 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: 2.43 (0.18), residues: 2220 helix: 2.73 (0.12), residues: 1680 sheet: -1.91 (0.34), residues: 204 loop : -2.15 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 77 HIS 0.007 0.001 HIS B 194 PHE 0.022 0.001 PHE L 31 TYR 0.040 0.001 TYR F 65 ARG 0.008 0.000 ARG D 52 Details of bonding type rmsd hydrogen bonds : bond 0.03072 ( 1392) hydrogen bonds : angle 3.24283 ( 4176) SS BOND : bond 0.00283 ( 36) SS BOND : angle 0.90613 ( 72) covalent geometry : bond 0.00279 (19008) covalent geometry : angle 0.62906 (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 363 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 275 time to evaluate : 2.378 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: 0.7942 (mtm110) cc_final: 0.7420 (mpp-170) REVERT: A 173 GLN cc_start: 0.9512 (tm-30) cc_final: 0.9190 (tm-30) REVERT: B 52 ARG cc_start: 0.8108 (mtm-85) cc_final: 0.7495 (mtm-85) REVERT: B 56 GLN cc_start: 0.9442 (mt0) cc_final: 0.8301 (mt0) REVERT: B 61 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8382 (mm-30) REVERT: B 91 TYR cc_start: 0.9236 (t80) cc_final: 0.8823 (t80) REVERT: B 173 GLN cc_start: 0.9539 (tm-30) cc_final: 0.9221 (tm-30) REVERT: B 188 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8375 (tppp) REVERT: C 34 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9184 (pp) REVERT: C 56 GLN cc_start: 0.9627 (mt0) cc_final: 0.8827 (mt0) REVERT: C 91 TYR cc_start: 0.8770 (t80) cc_final: 0.8315 (t80) REVERT: C 160 LEU cc_start: 0.9683 (tp) cc_final: 0.9404 (pp) REVERT: C 188 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8554 (tppp) REVERT: D 34 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9268 (pp) REVERT: D 56 GLN cc_start: 0.9569 (mt0) cc_final: 0.8503 (mt0) REVERT: D 188 LYS cc_start: 0.9271 (mmmm) cc_final: 0.8876 (mmmm) REVERT: E 56 GLN cc_start: 0.9422 (mt0) cc_final: 0.8659 (mt0) REVERT: E 61 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8261 (mm-30) REVERT: E 65 TYR cc_start: 0.9345 (t80) cc_final: 0.8736 (t80) REVERT: E 173 GLN cc_start: 0.9589 (tm-30) cc_final: 0.8933 (tm-30) REVERT: F 56 GLN cc_start: 0.9272 (pt0) cc_final: 0.9026 (pt0) REVERT: F 173 GLN cc_start: 0.9531 (tm-30) cc_final: 0.8867 (tm-30) REVERT: F 195 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8948 (pt0) REVERT: F 196 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8569 (m) REVERT: G 41 GLU cc_start: 0.8427 (pm20) cc_final: 0.8223 (pm20) REVERT: G 61 GLU cc_start: 0.8242 (tm-30) cc_final: 0.8021 (tm-30) REVERT: H 166 GLU cc_start: 0.9317 (tp30) cc_final: 0.9071 (tp30) REVERT: H 173 GLN cc_start: 0.9373 (tm-30) cc_final: 0.9157 (tm-30) REVERT: H 218 LEU cc_start: 0.9810 (OUTLIER) cc_final: 0.9591 (mm) REVERT: I 188 LYS cc_start: 0.9337 (mmmm) cc_final: 0.8932 (mmmm) REVERT: J 227 GLU cc_start: 0.9242 (mm-30) cc_final: 0.9028 (mm-30) REVERT: K 14 GLN cc_start: 0.8478 (pt0) cc_final: 0.8159 (pt0) REVERT: K 91 TYR cc_start: 0.8977 (t80) cc_final: 0.8517 (t80) REVERT: K 223 LEU cc_start: 0.9654 (OUTLIER) cc_final: 0.9416 (mp) REVERT: L 34 LEU cc_start: 0.9723 (tp) cc_final: 0.9417 (pp) REVERT: L 166 GLU cc_start: 0.9436 (tp30) cc_final: 0.9166 (tp30) REVERT: L 173 GLN cc_start: 0.9670 (OUTLIER) cc_final: 0.9464 (tt0) REVERT: L 188 LYS cc_start: 0.9430 (mmmm) cc_final: 0.8722 (tppp) outliers start: 88 outliers final: 69 residues processed: 343 average time/residue: 0.3101 time to fit residues: 159.5441 Evaluate side-chains 332 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 256 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 86 VAL 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 D residue 86 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 154 THR 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 34 LEU 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 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 195 GLN Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 54 ASN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 56 GLN 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 J residue 16 TYR Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 86 VAL 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 68 SER Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 86 VAL 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 88 THR Chi-restraints excluded: chain L residue 173 GLN Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 207 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 198 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 40.0000 chunk 179 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** B 224 ASN ** G 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.063631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.051456 restraints weight = 86649.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.052882 restraints weight = 38792.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.053916 restraints weight = 23426.294| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.9300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19044 Z= 0.160 Angle : 0.644 13.097 25872 Z= 0.320 Chirality : 0.039 0.310 2952 Planarity : 0.004 0.040 3096 Dihedral : 4.318 49.487 2446 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.22 % Allowed : 23.73 % Favored : 72.06 % 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: 2.43 (0.18), residues: 2220 helix: 2.71 (0.12), residues: 1680 sheet: -1.89 (0.34), residues: 204 loop : -2.03 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 77 HIS 0.004 0.001 HIS G 73 PHE 0.021 0.001 PHE L 31 TYR 0.034 0.001 TYR F 65 ARG 0.004 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03081 ( 1392) hydrogen bonds : angle 3.31449 ( 4176) SS BOND : bond 0.00293 ( 36) SS BOND : angle 0.96805 ( 72) covalent geometry : bond 0.00368 (19008) covalent geometry : angle 0.64248 (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 344 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 258 time to evaluate : 1.901 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 46 ASP cc_start: 0.8433 (p0) cc_final: 0.7892 (p0) REVERT: A 52 ARG cc_start: 0.7867 (mtm110) cc_final: 0.7353 (mpp-170) REVERT: A 173 GLN cc_start: 0.9523 (tm-30) cc_final: 0.9198 (tm-30) REVERT: B 52 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7683 (mpp-170) REVERT: B 61 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8353 (mm-30) REVERT: B 173 GLN cc_start: 0.9546 (tm-30) cc_final: 0.9226 (tm-30) REVERT: B 188 LYS cc_start: 0.9120 (mmmm) cc_final: 0.8800 (mmmm) REVERT: C 34 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9185 (pp) REVERT: C 56 GLN cc_start: 0.9632 (mt0) cc_final: 0.8819 (mt0) REVERT: C 91 TYR cc_start: 0.8856 (t80) cc_final: 0.8384 (t80) REVERT: C 160 LEU cc_start: 0.9699 (tp) cc_final: 0.9415 (pp) REVERT: C 188 LYS cc_start: 0.9227 (mmmm) cc_final: 0.8584 (tppp) REVERT: D 34 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9286 (pp) REVERT: D 56 GLN cc_start: 0.9583 (mt0) cc_final: 0.8521 (mt0) REVERT: D 188 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8874 (mmmm) REVERT: E 61 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8286 (mm-30) REVERT: E 173 GLN cc_start: 0.9603 (tm-30) cc_final: 0.8858 (tm-30) REVERT: F 56 GLN cc_start: 0.9317 (pt0) cc_final: 0.9075 (pt0) REVERT: F 173 GLN cc_start: 0.9529 (tm-30) cc_final: 0.9067 (tm-30) REVERT: F 196 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8577 (m) REVERT: G 47 GLU cc_start: 0.8268 (mp0) cc_final: 0.8063 (pm20) REVERT: H 166 GLU cc_start: 0.9317 (tp30) cc_final: 0.9059 (tp30) REVERT: H 173 GLN cc_start: 0.9386 (tm-30) cc_final: 0.9152 (tm-30) REVERT: H 218 LEU cc_start: 0.9804 (OUTLIER) cc_final: 0.9573 (mm) REVERT: I 188 LYS cc_start: 0.9343 (mmmm) cc_final: 0.8882 (mmmm) REVERT: K 91 TYR cc_start: 0.9039 (t80) cc_final: 0.8569 (t80) REVERT: K 223 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9408 (mp) REVERT: L 14 GLN cc_start: 0.8851 (pt0) cc_final: 0.8579 (pm20) REVERT: L 34 LEU cc_start: 0.9720 (tp) cc_final: 0.9433 (pp) REVERT: L 166 GLU cc_start: 0.9428 (tp30) cc_final: 0.9155 (tp30) REVERT: L 188 LYS cc_start: 0.9416 (mmmm) cc_final: 0.8705 (tppp) outliers start: 86 outliers final: 74 residues processed: 323 average time/residue: 0.3472 time to fit residues: 167.6460 Evaluate side-chains 328 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 249 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 86 VAL 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 55 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 154 THR 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 34 LEU 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 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 195 GLN Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 54 ASN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 56 GLN 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 J residue 16 TYR Chi-restraints excluded: chain J residue 52 ARG Chi-restraints excluded: chain J residue 55 THR 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 34 LEU 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 85 SER Chi-restraints excluded: chain K residue 86 VAL 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 55 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 53 optimal weight: 7.9990 chunk 184 optimal weight: 0.1980 chunk 167 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 109 optimal weight: 40.0000 chunk 112 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- 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** ** G 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.063078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.050919 restraints weight = 86454.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.052357 restraints weight = 38357.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.053389 restraints weight = 23244.040| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.9592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19044 Z= 0.177 Angle : 0.664 13.139 25872 Z= 0.331 Chirality : 0.039 0.384 2952 Planarity : 0.004 0.042 3096 Dihedral : 4.291 39.681 2446 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.22 % Allowed : 23.33 % Favored : 72.45 % 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: 2.35 (0.18), residues: 2220 helix: 2.65 (0.12), residues: 1680 sheet: -2.01 (0.34), residues: 204 loop : -1.95 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 77 HIS 0.005 0.001 HIS G 73 PHE 0.021 0.001 PHE L 31 TYR 0.033 0.001 TYR E 65 ARG 0.010 0.001 ARG D 52 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 1392) hydrogen bonds : angle 3.39217 ( 4176) SS BOND : bond 0.00300 ( 36) SS BOND : angle 0.99383 ( 72) covalent geometry : bond 0.00405 (19008) covalent geometry : angle 0.66245 (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 343 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 257 time to evaluate : 2.070 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: 0.7827 (mtm110) cc_final: 0.7299 (mpp-170) REVERT: B 52 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7521 (mtm180) REVERT: B 61 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8371 (mm-30) REVERT: B 188 LYS cc_start: 0.9126 (mmmm) cc_final: 0.8788 (mmmm) REVERT: C 34 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9202 (pp) REVERT: C 61 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8392 (mm-30) REVERT: C 91 TYR cc_start: 0.8957 (t80) cc_final: 0.8459 (t80) REVERT: C 160 LEU cc_start: 0.9720 (tp) cc_final: 0.9429 (pp) REVERT: C 188 LYS cc_start: 0.9245 (mmmm) cc_final: 0.8562 (tppp) REVERT: D 8 LYS cc_start: 0.9488 (mmtt) cc_final: 0.9221 (ptpp) REVERT: D 34 LEU cc_start: 0.9705 (tp) cc_final: 0.9283 (pp) REVERT: D 52 ARG cc_start: 0.9052 (ptp-110) cc_final: 0.8787 (ptp90) REVERT: D 56 GLN cc_start: 0.9584 (mt0) cc_final: 0.8530 (mt0) REVERT: D 188 LYS cc_start: 0.9278 (mmmm) cc_final: 0.8867 (mmmm) REVERT: E 61 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8246 (mm-30) REVERT: E 173 GLN cc_start: 0.9615 (tm-30) cc_final: 0.9336 (tm-30) REVERT: E 228 LEU cc_start: 0.9486 (pp) cc_final: 0.9244 (pp) REVERT: F 52 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7146 (mtm110) REVERT: F 56 GLN cc_start: 0.9364 (pt0) cc_final: 0.9133 (pt0) REVERT: F 196 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8637 (m) REVERT: G 47 GLU cc_start: 0.8281 (mp0) cc_final: 0.8069 (pm20) REVERT: G 52 ARG cc_start: 0.8825 (mmm-85) cc_final: 0.8574 (mmm-85) REVERT: H 166 GLU cc_start: 0.9322 (tp30) cc_final: 0.9066 (tp30) REVERT: H 173 GLN cc_start: 0.9398 (tm-30) cc_final: 0.9161 (tm-30) REVERT: H 218 LEU cc_start: 0.9806 (OUTLIER) cc_final: 0.9561 (mm) REVERT: I 56 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.9142 (mt0) REVERT: I 188 LYS cc_start: 0.9341 (mmmm) cc_final: 0.8877 (mmmm) REVERT: J 41 GLU cc_start: 0.8514 (tt0) cc_final: 0.7837 (tm-30) REVERT: K 14 GLN cc_start: 0.8388 (pt0) cc_final: 0.8140 (pt0) REVERT: K 91 TYR cc_start: 0.9058 (t80) cc_final: 0.8564 (t80) REVERT: K 188 LYS cc_start: 0.8917 (tppt) cc_final: 0.8653 (mmmm) REVERT: K 223 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9416 (mp) REVERT: L 34 LEU cc_start: 0.9720 (tp) cc_final: 0.9435 (pp) REVERT: L 166 GLU cc_start: 0.9423 (tp30) cc_final: 0.9151 (tp30) outliers start: 86 outliers final: 73 residues processed: 320 average time/residue: 0.3277 time to fit residues: 155.8562 Evaluate side-chains 325 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 247 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 86 VAL 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 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 154 THR 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 34 LEU 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 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 196 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 218 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 56 GLN Chi-restraints excluded: chain I residue 78 VAL 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 J residue 52 ARG Chi-restraints excluded: chain J residue 55 THR 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 34 LEU 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 85 SER Chi-restraints excluded: chain K residue 86 VAL 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 55 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 43 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 188 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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** ** G 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN ** K 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.064632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.052480 restraints weight = 84386.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.053933 restraints weight = 37549.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.054843 restraints weight = 22484.129| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.9633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19044 Z= 0.114 Angle : 0.658 14.016 25872 Z= 0.317 Chirality : 0.038 0.374 2952 Planarity : 0.004 0.042 3096 Dihedral : 4.156 43.505 2444 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.33 % Allowed : 24.36 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.34 (0.18), residues: 2220 helix: 2.62 (0.12), residues: 1680 sheet: -1.82 (0.35), residues: 204 loop : -1.99 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 77 HIS 0.004 0.001 HIS G 73 PHE 0.021 0.001 PHE L 31 TYR 0.022 0.001 TYR E 65 ARG 0.008 0.000 ARG D 52 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 1392) hydrogen bonds : angle 3.28452 ( 4176) SS BOND : bond 0.00261 ( 36) SS BOND : angle 0.83826 ( 72) covalent geometry : bond 0.00255 (19008) covalent geometry : angle 0.65705 (25800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5947.94 seconds wall clock time: 105 minutes 11.02 seconds (6311.02 seconds total)