Starting phenix.real_space_refine on Sun May 18 01:13:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qjh_18447/05_2025/8qjh_18447_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qjh_18447/05_2025/8qjh_18447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qjh_18447/05_2025/8qjh_18447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qjh_18447/05_2025/8qjh_18447.map" model { file = "/net/cci-nas-00/data/ceres_data/8qjh_18447/05_2025/8qjh_18447_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qjh_18447/05_2025/8qjh_18447_neut.cif" } resolution = 2.91 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 156 5.16 5 C 11052 2.51 5 N 2628 2.21 5 O 2748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16584 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1382 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 5.35, per 1000 atoms: 0.32 Number of scatterers: 16584 At special positions: 0 Unit cell: (99.45, 91.65, 142.35, 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 156 16.00 O 2748 8.00 N 2628 7.00 C 11052 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 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 179 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 179 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 179 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 179 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 179 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 173 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 173 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 173 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 173 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 168 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 168 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 168 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 168 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 168 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.37 Conformation dependent library (CDL) restraints added in 2.3 seconds 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4008 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 74.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 23 through 42 removed outlier: 4.142A pdb=" N GLU A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 99 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 157 removed outlier: 4.205A pdb=" N THR A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 217 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 23 through 42 removed outlier: 4.142A pdb=" N GLU B 41 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.517A pdb=" N VAL B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 99 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 130 through 157 removed outlier: 4.204A pdb=" N THR B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 217 Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 23 through 42 removed outlier: 4.142A pdb=" N GLU C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL C 63 " --> pdb=" O GLY C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 99 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 130 through 157 removed outlier: 4.205A pdb=" N THR C 134 " --> pdb=" O THR C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 217 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 23 through 42 removed outlier: 4.142A pdb=" N GLU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 removed outlier: 3.517A pdb=" N VAL D 63 " --> pdb=" O GLY D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 99 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 130 through 157 removed outlier: 4.206A pdb=" N THR D 134 " --> pdb=" O THR D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 217 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 23 through 42 removed outlier: 4.143A pdb=" N GLU E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER E 42 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL E 63 " --> pdb=" O GLY E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 99 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 130 through 157 removed outlier: 4.205A pdb=" N THR E 134 " --> pdb=" O THR E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 217 Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 23 through 42 removed outlier: 4.143A pdb=" N GLU F 41 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER F 42 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 99 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 130 through 157 removed outlier: 4.206A pdb=" N THR F 134 " --> pdb=" O THR F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 217 Processing helix chain 'G' and resid 18 through 23 Processing helix chain 'G' and resid 23 through 42 removed outlier: 4.142A pdb=" N GLU G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER G 42 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL G 63 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 99 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 130 through 157 removed outlier: 4.206A pdb=" N THR G 134 " --> pdb=" O THR G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 217 Processing helix chain 'H' and resid 18 through 23 Processing helix chain 'H' and resid 23 through 42 removed outlier: 4.143A pdb=" N GLU H 41 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 99 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 130 through 157 removed outlier: 4.206A pdb=" N THR H 134 " --> pdb=" O THR H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 217 Processing helix chain 'I' and resid 18 through 23 Processing helix chain 'I' and resid 23 through 42 removed outlier: 4.142A pdb=" N GLU I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER I 42 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL I 63 " --> pdb=" O GLY I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 99 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 130 through 157 removed outlier: 4.205A pdb=" N THR I 134 " --> pdb=" O THR I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 217 Processing helix chain 'J' and resid 18 through 23 Processing helix chain 'J' and resid 23 through 42 removed outlier: 4.143A pdb=" N GLU J 41 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL J 63 " --> pdb=" O GLY J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 99 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 130 through 157 removed outlier: 4.206A pdb=" N THR J 134 " --> pdb=" O THR J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 217 Processing helix chain 'K' and resid 18 through 23 Processing helix chain 'K' and resid 23 through 42 removed outlier: 4.143A pdb=" N GLU K 41 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER K 42 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL K 63 " --> pdb=" O GLY K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 99 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 130 through 157 removed outlier: 4.206A pdb=" N THR K 134 " --> pdb=" O THR K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 217 Processing helix chain 'L' and resid 18 through 23 Processing helix chain 'L' and resid 23 through 42 removed outlier: 4.143A pdb=" N GLU L 41 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER L 42 " --> pdb=" O VAL L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 removed outlier: 3.516A pdb=" N VAL L 63 " --> pdb=" O GLY L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 99 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 130 through 157 removed outlier: 4.205A pdb=" N THR L 134 " --> pdb=" O THR L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE A 52 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE B 52 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE C 52 " --> pdb=" O PHE C 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.924A pdb=" N ILE D 52 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.924A pdb=" N ILE E 52 " --> pdb=" O PHE E 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE F 52 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.924A pdb=" N ILE G 52 " --> pdb=" O PHE G 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE H 52 " --> pdb=" O PHE H 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE I 52 " --> pdb=" O PHE I 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE J 52 " --> pdb=" O PHE J 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 removed outlier: 3.923A pdb=" N ILE K 52 " --> pdb=" O PHE K 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.924A pdb=" N ILE L 52 " --> pdb=" O PHE L 180 " (cutoff:3.500A) 1224 hydrogen bonds defined for protein. 3636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.20 Time building geometry restraints manager: 5.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4908 1.35 - 1.46: 4449 1.46 - 1.58: 7479 1.58 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 17052 Sorted by residual: bond pdb=" C THR J 86 " pdb=" N PRO J 87 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.28e-02 6.10e+03 3.92e-01 bond pdb=" C THR K 86 " pdb=" N PRO K 87 " ideal model delta sigma weight residual 1.335 1.342 -0.008 1.28e-02 6.10e+03 3.61e-01 bond pdb=" C THR F 86 " pdb=" N PRO F 87 " ideal model delta sigma weight residual 1.335 1.342 -0.008 1.28e-02 6.10e+03 3.60e-01 bond pdb=" C THR I 86 " pdb=" N PRO I 87 " ideal model delta sigma weight residual 1.335 1.342 -0.008 1.28e-02 6.10e+03 3.44e-01 bond pdb=" C ARG I 183 " pdb=" O ARG I 183 " ideal model delta sigma weight residual 1.235 1.232 0.003 4.70e-03 4.53e+04 3.33e-01 ... (remaining 17047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 22857 1.06 - 2.12: 298 2.12 - 3.19: 89 3.19 - 4.25: 59 4.25 - 5.31: 13 Bond angle restraints: 23316 Sorted by residual: angle pdb=" CA CYS H 173 " pdb=" CB CYS H 173 " pdb=" SG CYS H 173 " ideal model delta sigma weight residual 114.40 110.74 3.66 2.30e+00 1.89e-01 2.53e+00 angle pdb=" CA CYS L 60 " pdb=" CB CYS L 60 " pdb=" SG CYS L 60 " ideal model delta sigma weight residual 114.40 110.74 3.66 2.30e+00 1.89e-01 2.53e+00 angle pdb=" CA CYS J 60 " pdb=" CB CYS J 60 " pdb=" SG CYS J 60 " ideal model delta sigma weight residual 114.40 110.75 3.65 2.30e+00 1.89e-01 2.52e+00 angle pdb=" CA CYS J 173 " pdb=" CB CYS J 173 " pdb=" SG CYS J 173 " ideal model delta sigma weight residual 114.40 110.76 3.64 2.30e+00 1.89e-01 2.51e+00 angle pdb=" CA CYS B 173 " pdb=" CB CYS B 173 " pdb=" SG CYS B 173 " ideal model delta sigma weight residual 114.40 110.76 3.64 2.30e+00 1.89e-01 2.51e+00 ... (remaining 23311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.53: 8512 8.53 - 17.07: 812 17.07 - 25.60: 312 25.60 - 34.14: 216 34.14 - 42.67: 60 Dihedral angle restraints: 9912 sinusoidal: 3756 harmonic: 6156 Sorted by residual: dihedral pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " pdb=" SG CYS B 173 " pdb=" CB CYS B 173 " ideal model delta sinusoidal sigma weight residual -86.00 -119.92 33.92 1 1.00e+01 1.00e-02 1.63e+01 dihedral pdb=" CB CYS E 60 " pdb=" SG CYS E 60 " pdb=" SG CYS E 173 " pdb=" CB CYS E 173 " ideal model delta sinusoidal sigma weight residual -86.00 -119.90 33.90 1 1.00e+01 1.00e-02 1.63e+01 dihedral pdb=" CB CYS K 60 " pdb=" SG CYS K 60 " pdb=" SG CYS K 173 " pdb=" CB CYS K 173 " ideal model delta sinusoidal sigma weight residual -86.00 -119.90 33.90 1 1.00e+01 1.00e-02 1.63e+01 ... (remaining 9909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 1537 0.022 - 0.045: 654 0.045 - 0.067: 412 0.067 - 0.089: 112 0.089 - 0.111: 81 Chirality restraints: 2796 Sorted by residual: chirality pdb=" CA THR C 86 " pdb=" N THR C 86 " pdb=" C THR C 86 " pdb=" CB THR C 86 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.11 2.00e-01 2.50e+01 3.10e-01 chirality pdb=" CA THR K 86 " pdb=" N THR K 86 " pdb=" C THR K 86 " pdb=" CB THR K 86 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.11 2.00e-01 2.50e+01 3.02e-01 chirality pdb=" CA THR D 86 " pdb=" N THR D 86 " pdb=" C THR D 86 " pdb=" CB THR D 86 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.11 2.00e-01 2.50e+01 2.98e-01 ... (remaining 2793 not shown) Planarity restraints: 2784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 171 " -0.014 5.00e-02 4.00e+02 2.18e-02 7.60e-01 pdb=" N PRO B 172 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO B 172 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 172 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 171 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.53e-01 pdb=" N PRO D 172 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO D 172 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 172 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 171 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.52e-01 pdb=" N PRO H 172 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO H 172 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO H 172 " -0.011 5.00e-02 4.00e+02 ... (remaining 2781 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3462 2.78 - 3.31: 17187 3.31 - 3.84: 29990 3.84 - 4.37: 32531 4.37 - 4.90: 57710 Nonbonded interactions: 140880 Sorted by model distance: nonbonded pdb=" O ASP A 46 " pdb=" OG SER A 50 " model vdw 2.248 3.040 nonbonded pdb=" O ASP H 46 " pdb=" OG SER H 50 " model vdw 2.248 3.040 nonbonded pdb=" O ASP F 46 " pdb=" OG SER F 50 " model vdw 2.248 3.040 nonbonded pdb=" O ASP I 46 " pdb=" OG SER I 50 " model vdw 2.248 3.040 nonbonded pdb=" O ASP G 46 " pdb=" OG SER G 50 " model vdw 2.249 3.040 ... (remaining 140875 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: 0.15 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 33.370 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 : 0.002 0.015 17088 Z= 0.080 Angle : 0.409 5.310 23388 Z= 0.205 Chirality : 0.036 0.111 2796 Planarity : 0.002 0.022 2784 Dihedral : 9.688 42.675 5796 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.29 % Allowed : 5.81 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.25 (0.18), residues: 2028 helix: 3.36 (0.12), residues: 1392 sheet: 1.26 (0.48), residues: 132 loop : -1.33 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 77 HIS 0.001 0.000 HIS F 73 PHE 0.005 0.001 PHE E 180 TYR 0.004 0.001 TYR G 151 ARG 0.001 0.000 ARG D 183 Details of bonding type rmsd hydrogen bonds : bond 0.11055 ( 1224) hydrogen bonds : angle 4.64988 ( 3636) SS BOND : bond 0.00087 ( 36) SS BOND : angle 0.70696 ( 72) covalent geometry : bond 0.00175 (17052) covalent geometry : angle 0.40746 (23316) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 486 time to evaluate : 1.779 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 47 GLU cc_start: 0.8236 (pt0) cc_final: 0.7999 (pt0) REVERT: A 66 ASP cc_start: 0.8381 (t70) cc_final: 0.8039 (t0) REVERT: A 215 ARG cc_start: 0.8444 (tpp-160) cc_final: 0.8018 (tpt170) REVERT: B 30 ILE cc_start: 0.9400 (mt) cc_final: 0.9135 (mp) REVERT: B 47 GLU cc_start: 0.8248 (pt0) cc_final: 0.7971 (pt0) REVERT: B 66 ASP cc_start: 0.8315 (t70) cc_final: 0.8014 (t0) REVERT: B 142 ARG cc_start: 0.8744 (ttm170) cc_final: 0.7972 (ttm-80) REVERT: B 162 MET cc_start: 0.8610 (mmt) cc_final: 0.8211 (mmt) REVERT: B 215 ARG cc_start: 0.8413 (tpp-160) cc_final: 0.8057 (tpt170) REVERT: C 47 GLU cc_start: 0.8254 (pt0) cc_final: 0.8025 (pt0) REVERT: C 66 ASP cc_start: 0.8354 (t70) cc_final: 0.8069 (t0) REVERT: C 215 ARG cc_start: 0.8450 (tpp-160) cc_final: 0.8116 (tpt170) REVERT: D 47 GLU cc_start: 0.8208 (pt0) cc_final: 0.7986 (pt0) REVERT: D 66 ASP cc_start: 0.8355 (t70) cc_final: 0.8026 (t0) REVERT: D 215 ARG cc_start: 0.8403 (tpp-160) cc_final: 0.8076 (tpt170) REVERT: E 30 ILE cc_start: 0.9399 (mt) cc_final: 0.9135 (mp) REVERT: E 47 GLU cc_start: 0.8243 (pt0) cc_final: 0.7993 (pt0) REVERT: E 66 ASP cc_start: 0.8313 (t70) cc_final: 0.8010 (t0) REVERT: E 142 ARG cc_start: 0.8745 (ttm170) cc_final: 0.7977 (ttm-80) REVERT: E 162 MET cc_start: 0.8605 (mmt) cc_final: 0.8209 (mmt) REVERT: E 215 ARG cc_start: 0.8413 (tpp-160) cc_final: 0.8059 (tpt170) REVERT: F 47 GLU cc_start: 0.8262 (pt0) cc_final: 0.7971 (pt0) REVERT: F 66 ASP cc_start: 0.8355 (t70) cc_final: 0.8054 (t0) REVERT: F 162 MET cc_start: 0.8586 (mmt) cc_final: 0.8355 (mmt) REVERT: F 215 ARG cc_start: 0.8451 (tpp-160) cc_final: 0.8119 (tpt170) REVERT: G 47 GLU cc_start: 0.8228 (pt0) cc_final: 0.7984 (pt0) REVERT: G 66 ASP cc_start: 0.8355 (t70) cc_final: 0.8041 (t0) REVERT: G 215 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.8082 (tpt170) REVERT: H 30 ILE cc_start: 0.9399 (mt) cc_final: 0.9134 (mp) REVERT: H 47 GLU cc_start: 0.8229 (pt0) cc_final: 0.7986 (pt0) REVERT: H 66 ASP cc_start: 0.8323 (t70) cc_final: 0.8007 (t0) REVERT: H 142 ARG cc_start: 0.8744 (ttm170) cc_final: 0.8072 (ttm-80) REVERT: H 162 MET cc_start: 0.8616 (mmt) cc_final: 0.8221 (mmt) REVERT: H 215 ARG cc_start: 0.8401 (tpp-160) cc_final: 0.8044 (tpt170) REVERT: I 47 GLU cc_start: 0.8244 (pt0) cc_final: 0.8020 (pt0) REVERT: I 66 ASP cc_start: 0.8362 (t70) cc_final: 0.8067 (t0) REVERT: I 162 MET cc_start: 0.8584 (mmt) cc_final: 0.8357 (mmt) REVERT: I 215 ARG cc_start: 0.8451 (tpp-160) cc_final: 0.8097 (tpt170) REVERT: J 47 GLU cc_start: 0.8230 (pt0) cc_final: 0.8005 (pt0) REVERT: J 66 ASP cc_start: 0.8369 (t70) cc_final: 0.8039 (t0) REVERT: J 215 ARG cc_start: 0.8411 (tpp-160) cc_final: 0.8071 (tpt170) REVERT: K 30 ILE cc_start: 0.9400 (mt) cc_final: 0.9130 (mp) REVERT: K 47 GLU cc_start: 0.8241 (pt0) cc_final: 0.7991 (pt0) REVERT: K 66 ASP cc_start: 0.8323 (t70) cc_final: 0.8010 (t0) REVERT: K 142 ARG cc_start: 0.8738 (ttm170) cc_final: 0.8061 (ttm-80) REVERT: K 162 MET cc_start: 0.8614 (mmt) cc_final: 0.8215 (mmt) REVERT: K 215 ARG cc_start: 0.8403 (tpp-160) cc_final: 0.8047 (tpt170) REVERT: L 47 GLU cc_start: 0.8246 (pt0) cc_final: 0.7989 (pt0) REVERT: L 66 ASP cc_start: 0.8374 (t70) cc_final: 0.8094 (t0) REVERT: L 133 TRP cc_start: 0.7959 (m100) cc_final: 0.7740 (m-10) REVERT: L 162 MET cc_start: 0.8581 (mmt) cc_final: 0.8348 (mmt) REVERT: L 215 ARG cc_start: 0.8461 (tpp-160) cc_final: 0.8104 (tpt170) outliers start: 24 outliers final: 0 residues processed: 498 average time/residue: 1.1314 time to fit residues: 629.7727 Evaluate side-chains 297 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 A 175 ASN B 54 ASN B 57 GLN B 175 ASN C 54 ASN C 57 GLN C 175 ASN D 54 ASN D 57 GLN D 175 ASN E 54 ASN E 57 GLN E 175 ASN F 54 ASN F 57 GLN F 175 ASN G 54 ASN G 57 GLN G 175 ASN H 54 ASN H 57 GLN H 175 ASN I 54 ASN I 57 GLN I 175 ASN J 54 ASN J 57 GLN J 175 ASN K 54 ASN K 57 GLN K 175 ASN L 54 ASN L 57 GLN L 94 HIS L 175 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.094583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.073257 restraints weight = 30955.323| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.13 r_work: 0.2918 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17088 Z= 0.188 Angle : 0.547 5.503 23388 Z= 0.288 Chirality : 0.044 0.201 2796 Planarity : 0.003 0.017 2784 Dihedral : 3.315 11.182 2232 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.52 % Allowed : 13.60 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.98 (0.17), residues: 2028 helix: 3.17 (0.12), residues: 1404 sheet: 1.31 (0.48), residues: 132 loop : -1.67 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 44 HIS 0.004 0.001 HIS H 97 PHE 0.011 0.002 PHE G 190 TYR 0.014 0.001 TYR F 211 ARG 0.005 0.001 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 1224) hydrogen bonds : angle 3.52154 ( 3636) SS BOND : bond 0.00128 ( 36) SS BOND : angle 1.16229 ( 72) covalent geometry : bond 0.00442 (17052) covalent geometry : angle 0.54376 (23316) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 319 time to evaluate : 1.880 Fit side-chains REVERT: A 66 ASP cc_start: 0.9095 (t70) cc_final: 0.8762 (t0) REVERT: A 133 TRP cc_start: 0.7523 (OUTLIER) cc_final: 0.7280 (m-10) REVERT: A 169 ASP cc_start: 0.8716 (p0) cc_final: 0.8501 (p0) REVERT: A 215 ARG cc_start: 0.8740 (tpp-160) cc_final: 0.8094 (tpt170) REVERT: B 47 GLU cc_start: 0.8794 (pt0) cc_final: 0.8546 (pt0) REVERT: B 66 ASP cc_start: 0.9025 (t70) cc_final: 0.8570 (t0) REVERT: B 133 TRP cc_start: 0.7482 (OUTLIER) cc_final: 0.7233 (m-10) REVERT: B 162 MET cc_start: 0.9079 (mmt) cc_final: 0.8868 (mmt) REVERT: B 169 ASP cc_start: 0.8868 (p0) cc_final: 0.8615 (p0) REVERT: B 215 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8056 (tpt170) REVERT: C 46 ASP cc_start: 0.8966 (p0) cc_final: 0.8707 (p0) REVERT: C 47 GLU cc_start: 0.8808 (pt0) cc_final: 0.8587 (pt0) REVERT: C 66 ASP cc_start: 0.9070 (t70) cc_final: 0.8696 (t0) REVERT: C 93 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8939 (mmm) REVERT: C 133 TRP cc_start: 0.7535 (OUTLIER) cc_final: 0.7326 (m-10) REVERT: C 203 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9169 (mp) REVERT: C 215 ARG cc_start: 0.8635 (tpp-160) cc_final: 0.8167 (tpt170) REVERT: D 66 ASP cc_start: 0.9077 (t70) cc_final: 0.8747 (t0) REVERT: D 133 TRP cc_start: 0.7489 (OUTLIER) cc_final: 0.7223 (m-10) REVERT: D 169 ASP cc_start: 0.8732 (p0) cc_final: 0.8518 (p0) REVERT: D 211 TYR cc_start: 0.8604 (t80) cc_final: 0.8380 (t80) REVERT: D 215 ARG cc_start: 0.8663 (tpp-160) cc_final: 0.8116 (tpt170) REVERT: E 47 GLU cc_start: 0.8783 (pt0) cc_final: 0.8533 (pt0) REVERT: E 66 ASP cc_start: 0.9036 (t70) cc_final: 0.8582 (t0) REVERT: E 133 TRP cc_start: 0.7483 (OUTLIER) cc_final: 0.7237 (m-10) REVERT: E 162 MET cc_start: 0.9076 (mmt) cc_final: 0.8869 (mmt) REVERT: E 169 ASP cc_start: 0.8886 (p0) cc_final: 0.8643 (p0) REVERT: E 215 ARG cc_start: 0.8610 (tpp-160) cc_final: 0.8068 (tpt170) REVERT: F 46 ASP cc_start: 0.8960 (p0) cc_final: 0.8693 (p0) REVERT: F 47 GLU cc_start: 0.8798 (pt0) cc_final: 0.8558 (pt0) REVERT: F 66 ASP cc_start: 0.9075 (t70) cc_final: 0.8704 (t0) REVERT: F 93 MET cc_start: 0.9413 (OUTLIER) cc_final: 0.8802 (mmm) REVERT: F 133 TRP cc_start: 0.7500 (OUTLIER) cc_final: 0.7294 (m-10) REVERT: F 203 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9164 (mp) REVERT: F 215 ARG cc_start: 0.8636 (tpp-160) cc_final: 0.8160 (tpt170) REVERT: G 66 ASP cc_start: 0.9069 (t70) cc_final: 0.8740 (t0) REVERT: G 133 TRP cc_start: 0.7508 (OUTLIER) cc_final: 0.7240 (m-10) REVERT: G 169 ASP cc_start: 0.8705 (p0) cc_final: 0.8491 (p0) REVERT: G 211 TYR cc_start: 0.8596 (t80) cc_final: 0.8335 (t80) REVERT: G 215 ARG cc_start: 0.8679 (tpp-160) cc_final: 0.8129 (tpt170) REVERT: H 47 GLU cc_start: 0.8788 (pt0) cc_final: 0.8539 (pt0) REVERT: H 66 ASP cc_start: 0.9044 (t70) cc_final: 0.8589 (t0) REVERT: H 133 TRP cc_start: 0.7507 (OUTLIER) cc_final: 0.7244 (m-10) REVERT: H 162 MET cc_start: 0.9092 (mmt) cc_final: 0.8749 (mmt) REVERT: H 169 ASP cc_start: 0.8899 (p0) cc_final: 0.8648 (p0) REVERT: H 215 ARG cc_start: 0.8638 (tpp-160) cc_final: 0.8055 (tpt170) REVERT: I 46 ASP cc_start: 0.8956 (p0) cc_final: 0.8716 (p0) REVERT: I 47 GLU cc_start: 0.8818 (pt0) cc_final: 0.8606 (pt0) REVERT: I 66 ASP cc_start: 0.9087 (t70) cc_final: 0.8721 (t0) REVERT: I 93 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8949 (mmm) REVERT: I 133 TRP cc_start: 0.7511 (OUTLIER) cc_final: 0.7304 (m-10) REVERT: I 215 ARG cc_start: 0.8596 (tpp-160) cc_final: 0.8150 (tpt170) REVERT: J 66 ASP cc_start: 0.9086 (t70) cc_final: 0.8753 (t0) REVERT: J 133 TRP cc_start: 0.7491 (OUTLIER) cc_final: 0.7248 (m-10) REVERT: J 169 ASP cc_start: 0.8738 (p0) cc_final: 0.8527 (p0) REVERT: J 211 TYR cc_start: 0.8584 (t80) cc_final: 0.8357 (t80) REVERT: J 215 ARG cc_start: 0.8660 (tpp-160) cc_final: 0.8113 (tpt170) REVERT: K 47 GLU cc_start: 0.8783 (pt0) cc_final: 0.8533 (pt0) REVERT: K 66 ASP cc_start: 0.9043 (t70) cc_final: 0.8582 (t0) REVERT: K 133 TRP cc_start: 0.7477 (OUTLIER) cc_final: 0.7235 (m-10) REVERT: K 146 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8830 (mm-30) REVERT: K 162 MET cc_start: 0.9069 (mmt) cc_final: 0.8721 (mmt) REVERT: K 169 ASP cc_start: 0.8899 (p0) cc_final: 0.8650 (p0) REVERT: K 215 ARG cc_start: 0.8619 (tpp-160) cc_final: 0.8051 (tpt170) REVERT: L 46 ASP cc_start: 0.8958 (p0) cc_final: 0.8708 (p0) REVERT: L 47 GLU cc_start: 0.8802 (pt0) cc_final: 0.8585 (pt0) REVERT: L 66 ASP cc_start: 0.9090 (t70) cc_final: 0.8721 (t0) REVERT: L 93 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9050 (mmm) REVERT: L 94 HIS cc_start: 0.8793 (t70) cc_final: 0.8498 (t-90) REVERT: L 215 ARG cc_start: 0.8628 (tpp-160) cc_final: 0.8153 (tpt170) outliers start: 84 outliers final: 21 residues processed: 371 average time/residue: 1.1259 time to fit residues: 467.1672 Evaluate side-chains 319 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 281 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 133 TRP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 133 TRP Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 175 ASN Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 133 TRP Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 133 TRP Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 133 TRP Chi-restraints excluded: chain J residue 175 ASN Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 133 TRP Chi-restraints excluded: chain K residue 175 ASN Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 118 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 192 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 106 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN B 54 ASN B 175 ASN C 54 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN D 175 ASN E 54 ASN E 175 ASN F 54 ASN F 97 HIS F 175 ASN G 175 ASN H 54 ASN H 175 ASN I 54 ASN ** I 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN ** J 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN K 54 ASN K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.094786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.074121 restraints weight = 31104.522| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.18 r_work: 0.2938 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17088 Z= 0.118 Angle : 0.484 5.240 23388 Z= 0.258 Chirality : 0.042 0.219 2796 Planarity : 0.003 0.020 2784 Dihedral : 3.287 10.473 2232 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.92 % Allowed : 17.26 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.91 (0.17), residues: 2028 helix: 3.12 (0.12), residues: 1404 sheet: 0.87 (0.44), residues: 132 loop : -1.59 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 133 HIS 0.003 0.001 HIS G 97 PHE 0.009 0.001 PHE E 180 TYR 0.008 0.001 TYR L 211 ARG 0.003 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 1224) hydrogen bonds : angle 3.31558 ( 3636) SS BOND : bond 0.00105 ( 36) SS BOND : angle 0.76477 ( 72) covalent geometry : bond 0.00266 (17052) covalent geometry : angle 0.48243 (23316) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 318 time to evaluate : 1.973 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.9040 (t70) cc_final: 0.8742 (t0) REVERT: A 93 MET cc_start: 0.9039 (mmt) cc_final: 0.8796 (mmt) REVERT: A 133 TRP cc_start: 0.7470 (OUTLIER) cc_final: 0.7261 (m-10) REVERT: A 215 ARG cc_start: 0.8741 (tpp-160) cc_final: 0.8137 (tpt170) REVERT: B 47 GLU cc_start: 0.8787 (pt0) cc_final: 0.8585 (pt0) REVERT: B 66 ASP cc_start: 0.8991 (t70) cc_final: 0.8592 (t0) REVERT: B 93 MET cc_start: 0.9336 (tpp) cc_final: 0.9051 (mtp) REVERT: B 133 TRP cc_start: 0.7440 (OUTLIER) cc_final: 0.7196 (m-10) REVERT: B 169 ASP cc_start: 0.8837 (p0) cc_final: 0.8576 (p0) REVERT: B 215 ARG cc_start: 0.8575 (tpp-160) cc_final: 0.8065 (tpt170) REVERT: C 46 ASP cc_start: 0.8981 (p0) cc_final: 0.8697 (p0) REVERT: C 47 GLU cc_start: 0.8753 (pt0) cc_final: 0.8548 (pt0) REVERT: C 66 ASP cc_start: 0.9040 (t70) cc_final: 0.8673 (t0) REVERT: C 93 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9062 (mmt) REVERT: C 133 TRP cc_start: 0.7515 (OUTLIER) cc_final: 0.7314 (m-10) REVERT: C 203 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9126 (mp) REVERT: C 215 ARG cc_start: 0.8652 (tpp-160) cc_final: 0.8196 (tpt170) REVERT: D 66 ASP cc_start: 0.9013 (t70) cc_final: 0.8711 (t0) REVERT: D 133 TRP cc_start: 0.7401 (OUTLIER) cc_final: 0.7161 (m-10) REVERT: D 211 TYR cc_start: 0.8590 (t80) cc_final: 0.8347 (t80) REVERT: D 215 ARG cc_start: 0.8644 (tpp-160) cc_final: 0.8109 (tpt170) REVERT: E 47 GLU cc_start: 0.8775 (pt0) cc_final: 0.8573 (pt0) REVERT: E 66 ASP cc_start: 0.8992 (t70) cc_final: 0.8595 (t0) REVERT: E 93 MET cc_start: 0.9364 (tpp) cc_final: 0.9094 (mtp) REVERT: E 133 TRP cc_start: 0.7437 (OUTLIER) cc_final: 0.7223 (m-10) REVERT: E 169 ASP cc_start: 0.8848 (p0) cc_final: 0.8600 (p0) REVERT: E 215 ARG cc_start: 0.8583 (tpp-160) cc_final: 0.8063 (tpt170) REVERT: F 46 ASP cc_start: 0.8993 (p0) cc_final: 0.8705 (p0) REVERT: F 47 GLU cc_start: 0.8755 (pt0) cc_final: 0.8546 (pt0) REVERT: F 66 ASP cc_start: 0.9031 (t70) cc_final: 0.8666 (t0) REVERT: F 93 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.8968 (mmm) REVERT: F 133 TRP cc_start: 0.7486 (OUTLIER) cc_final: 0.7282 (m-10) REVERT: F 203 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9123 (mp) REVERT: F 215 ARG cc_start: 0.8635 (tpp-160) cc_final: 0.8194 (tpt170) REVERT: G 66 ASP cc_start: 0.9024 (t70) cc_final: 0.8722 (t0) REVERT: G 133 TRP cc_start: 0.7417 (OUTLIER) cc_final: 0.7181 (m-10) REVERT: G 169 ASP cc_start: 0.8761 (p0) cc_final: 0.8556 (p0) REVERT: G 211 TYR cc_start: 0.8581 (t80) cc_final: 0.8329 (t80) REVERT: G 215 ARG cc_start: 0.8670 (tpp-160) cc_final: 0.8130 (tpt170) REVERT: H 47 GLU cc_start: 0.8776 (pt0) cc_final: 0.8572 (pt0) REVERT: H 66 ASP cc_start: 0.9014 (t70) cc_final: 0.8616 (t0) REVERT: H 133 TRP cc_start: 0.7450 (OUTLIER) cc_final: 0.7208 (m-10) REVERT: H 169 ASP cc_start: 0.8895 (p0) cc_final: 0.8632 (p0) REVERT: H 215 ARG cc_start: 0.8592 (tpp-160) cc_final: 0.8062 (tpt170) REVERT: I 20 ILE cc_start: 0.8621 (mp) cc_final: 0.8298 (mp) REVERT: I 46 ASP cc_start: 0.8977 (p0) cc_final: 0.8693 (p0) REVERT: I 66 ASP cc_start: 0.9032 (t70) cc_final: 0.8664 (t0) REVERT: I 93 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9058 (mmt) REVERT: I 133 TRP cc_start: 0.7496 (OUTLIER) cc_final: 0.7295 (m-10) REVERT: I 215 ARG cc_start: 0.8643 (tpp-160) cc_final: 0.8177 (tpt170) REVERT: J 66 ASP cc_start: 0.9040 (t70) cc_final: 0.8745 (t0) REVERT: J 133 TRP cc_start: 0.7435 (OUTLIER) cc_final: 0.7223 (m-10) REVERT: J 169 ASP cc_start: 0.8770 (p0) cc_final: 0.8552 (p0) REVERT: J 211 TYR cc_start: 0.8586 (t80) cc_final: 0.8339 (t80) REVERT: J 215 ARG cc_start: 0.8672 (tpp-160) cc_final: 0.8129 (tpt170) REVERT: K 47 GLU cc_start: 0.8790 (pt0) cc_final: 0.8588 (pt0) REVERT: K 66 ASP cc_start: 0.9000 (t70) cc_final: 0.8604 (t0) REVERT: K 133 TRP cc_start: 0.7448 (OUTLIER) cc_final: 0.7207 (m-10) REVERT: K 169 ASP cc_start: 0.8898 (p0) cc_final: 0.8642 (p0) REVERT: K 215 ARG cc_start: 0.8596 (tpp-160) cc_final: 0.8054 (tpt170) REVERT: L 20 ILE cc_start: 0.8617 (mp) cc_final: 0.8293 (mp) REVERT: L 46 ASP cc_start: 0.8975 (p0) cc_final: 0.8683 (p0) REVERT: L 47 GLU cc_start: 0.8759 (pt0) cc_final: 0.8550 (pt0) REVERT: L 66 ASP cc_start: 0.9055 (t70) cc_final: 0.8690 (t0) REVERT: L 93 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.9101 (mmt) REVERT: L 94 HIS cc_start: 0.8725 (t70) cc_final: 0.8504 (t70) REVERT: L 215 ARG cc_start: 0.8626 (tpp-160) cc_final: 0.8177 (tpt170) outliers start: 73 outliers final: 14 residues processed: 354 average time/residue: 1.1753 time to fit residues: 465.4957 Evaluate side-chains 317 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 286 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 133 TRP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 133 TRP Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 133 TRP Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 133 TRP Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 133 TRP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 133 TRP Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 chunk 81 optimal weight: 0.1980 chunk 76 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN A 205 ASN B 54 ASN B 97 HIS B 175 ASN C 54 ASN C 175 ASN D 97 HIS D 175 ASN D 205 ASN E 54 ASN E 97 HIS F 54 ASN F 97 HIS F 175 ASN G 97 HIS G 175 ASN G 205 ASN H 54 ASN H 97 HIS H 175 ASN I 54 ASN I 175 ASN J 175 ASN J 205 ASN K 54 ASN K 97 HIS K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.093412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.072286 restraints weight = 31244.877| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.17 r_work: 0.2898 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17088 Z= 0.179 Angle : 0.506 5.323 23388 Z= 0.267 Chirality : 0.043 0.233 2796 Planarity : 0.003 0.017 2784 Dihedral : 3.265 10.511 2232 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.11 % Allowed : 17.53 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.95 (0.17), residues: 2028 helix: 3.12 (0.12), residues: 1404 sheet: 0.98 (0.45), residues: 132 loop : -1.51 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 44 HIS 0.005 0.001 HIS I 97 PHE 0.011 0.001 PHE I 68 TYR 0.010 0.001 TYR G 65 ARG 0.006 0.000 ARG J 22 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 1224) hydrogen bonds : angle 3.21476 ( 3636) SS BOND : bond 0.00171 ( 36) SS BOND : angle 0.85832 ( 72) covalent geometry : bond 0.00422 (17052) covalent geometry : angle 0.50496 (23316) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 321 time to evaluate : 2.101 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8580 (mp) cc_final: 0.8298 (mp) REVERT: A 66 ASP cc_start: 0.9159 (t70) cc_final: 0.8852 (t0) REVERT: A 133 TRP cc_start: 0.7474 (OUTLIER) cc_final: 0.7263 (m-10) REVERT: A 169 ASP cc_start: 0.8739 (p0) cc_final: 0.8520 (p0) REVERT: A 215 ARG cc_start: 0.8697 (tpp-160) cc_final: 0.8140 (tpt170) REVERT: B 47 GLU cc_start: 0.8824 (pt0) cc_final: 0.8598 (pt0) REVERT: B 66 ASP cc_start: 0.9075 (t70) cc_final: 0.8686 (t0) REVERT: B 93 MET cc_start: 0.9368 (tpp) cc_final: 0.9070 (mtp) REVERT: B 133 TRP cc_start: 0.7437 (OUTLIER) cc_final: 0.7229 (m-10) REVERT: B 169 ASP cc_start: 0.8827 (p0) cc_final: 0.8554 (p0) REVERT: B 215 ARG cc_start: 0.8582 (tpp-160) cc_final: 0.8075 (tpt170) REVERT: C 20 ILE cc_start: 0.8630 (mp) cc_final: 0.8322 (mp) REVERT: C 46 ASP cc_start: 0.9051 (p0) cc_final: 0.8769 (p0) REVERT: C 66 ASP cc_start: 0.9119 (t70) cc_final: 0.8715 (t0) REVERT: C 93 MET cc_start: 0.9404 (OUTLIER) cc_final: 0.8891 (mmm) REVERT: C 203 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9136 (mp) REVERT: C 215 ARG cc_start: 0.8629 (tpp-160) cc_final: 0.8190 (tpt170) REVERT: D 66 ASP cc_start: 0.9139 (t70) cc_final: 0.8817 (t0) REVERT: D 133 TRP cc_start: 0.7413 (OUTLIER) cc_final: 0.7182 (m-10) REVERT: D 169 ASP cc_start: 0.8776 (p0) cc_final: 0.8562 (p0) REVERT: D 211 TYR cc_start: 0.8566 (t80) cc_final: 0.8315 (t80) REVERT: D 215 ARG cc_start: 0.8638 (tpp-160) cc_final: 0.8119 (tpt170) REVERT: E 47 GLU cc_start: 0.8821 (pt0) cc_final: 0.8593 (pt0) REVERT: E 66 ASP cc_start: 0.9078 (t70) cc_final: 0.8689 (t0) REVERT: E 93 MET cc_start: 0.9383 (tpp) cc_final: 0.9094 (mtp) REVERT: E 133 TRP cc_start: 0.7433 (OUTLIER) cc_final: 0.7222 (m-10) REVERT: E 169 ASP cc_start: 0.8863 (p0) cc_final: 0.8603 (p0) REVERT: E 215 ARG cc_start: 0.8571 (tpp-160) cc_final: 0.8082 (tpt170) REVERT: F 46 ASP cc_start: 0.9034 (p0) cc_final: 0.8770 (p0) REVERT: F 47 GLU cc_start: 0.8802 (pt0) cc_final: 0.8574 (pt0) REVERT: F 66 ASP cc_start: 0.9111 (t70) cc_final: 0.8704 (t0) REVERT: F 93 MET cc_start: 0.9435 (OUTLIER) cc_final: 0.9005 (mmm) REVERT: F 133 TRP cc_start: 0.7481 (OUTLIER) cc_final: 0.7278 (m-10) REVERT: F 203 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9134 (mp) REVERT: F 215 ARG cc_start: 0.8634 (tpp-160) cc_final: 0.8189 (tpt170) REVERT: G 66 ASP cc_start: 0.9131 (t70) cc_final: 0.8813 (t0) REVERT: G 133 TRP cc_start: 0.7428 (OUTLIER) cc_final: 0.7198 (m-10) REVERT: G 211 TYR cc_start: 0.8544 (t80) cc_final: 0.8287 (t80) REVERT: G 215 ARG cc_start: 0.8663 (tpp-160) cc_final: 0.8132 (tpt170) REVERT: H 47 GLU cc_start: 0.8836 (pt0) cc_final: 0.8610 (pt0) REVERT: H 66 ASP cc_start: 0.9100 (t70) cc_final: 0.8712 (t0) REVERT: H 93 MET cc_start: 0.9422 (tpp) cc_final: 0.9078 (mtp) REVERT: H 133 TRP cc_start: 0.7461 (OUTLIER) cc_final: 0.7228 (m-10) REVERT: H 169 ASP cc_start: 0.8876 (p0) cc_final: 0.8607 (p0) REVERT: H 215 ARG cc_start: 0.8612 (tpp-160) cc_final: 0.8075 (tpt170) REVERT: I 20 ILE cc_start: 0.8641 (mp) cc_final: 0.8346 (mp) REVERT: I 46 ASP cc_start: 0.8987 (p0) cc_final: 0.8719 (p0) REVERT: I 66 ASP cc_start: 0.9127 (t70) cc_final: 0.8734 (t0) REVERT: I 93 MET cc_start: 0.9404 (OUTLIER) cc_final: 0.8888 (mmm) REVERT: I 133 TRP cc_start: 0.7468 (OUTLIER) cc_final: 0.7265 (m-10) REVERT: I 215 ARG cc_start: 0.8617 (tpp-160) cc_final: 0.8155 (tpt170) REVERT: J 66 ASP cc_start: 0.9155 (t70) cc_final: 0.8838 (t0) REVERT: J 133 TRP cc_start: 0.7455 (OUTLIER) cc_final: 0.7249 (m-10) REVERT: J 211 TYR cc_start: 0.8555 (t80) cc_final: 0.8299 (t80) REVERT: J 215 ARG cc_start: 0.8679 (tpp-160) cc_final: 0.8136 (tpt170) REVERT: K 47 GLU cc_start: 0.8850 (pt0) cc_final: 0.8627 (pt0) REVERT: K 66 ASP cc_start: 0.9093 (t70) cc_final: 0.8702 (t0) REVERT: K 93 MET cc_start: 0.9403 (tpp) cc_final: 0.9054 (mtp) REVERT: K 97 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7133 (t70) REVERT: K 133 TRP cc_start: 0.7455 (OUTLIER) cc_final: 0.7222 (m-10) REVERT: K 169 ASP cc_start: 0.8881 (p0) cc_final: 0.8618 (p0) REVERT: K 215 ARG cc_start: 0.8592 (tpp-160) cc_final: 0.8070 (tpt170) REVERT: L 20 ILE cc_start: 0.8635 (mp) cc_final: 0.8340 (mp) REVERT: L 46 ASP cc_start: 0.9039 (p0) cc_final: 0.8770 (p0) REVERT: L 66 ASP cc_start: 0.9123 (t70) cc_final: 0.8723 (t0) REVERT: L 93 MET cc_start: 0.9375 (OUTLIER) cc_final: 0.9127 (mmt) REVERT: L 94 HIS cc_start: 0.8748 (t70) cc_final: 0.8507 (t70) REVERT: L 215 ARG cc_start: 0.8616 (tpp-160) cc_final: 0.8159 (tpt170) outliers start: 95 outliers final: 30 residues processed: 380 average time/residue: 1.1401 time to fit residues: 486.4420 Evaluate side-chains 332 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 285 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 133 TRP Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 133 TRP Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 133 TRP Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 133 TRP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 133 TRP Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 214 ILE Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 118 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 140 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 175 ASN B 54 ASN B 97 HIS B 175 ASN C 54 ASN C 175 ASN D 54 ASN D 97 HIS D 175 ASN E 54 ASN E 97 HIS E 175 ASN F 54 ASN F 97 HIS F 175 ASN G 54 ASN G 97 HIS G 175 ASN H 54 ASN H 97 HIS H 175 ASN I 54 ASN I 175 ASN J 54 ASN J 175 ASN K 54 ASN K 97 HIS K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.094771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.073773 restraints weight = 31457.285| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.18 r_work: 0.2920 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17088 Z= 0.115 Angle : 0.472 5.197 23388 Z= 0.251 Chirality : 0.042 0.248 2796 Planarity : 0.003 0.017 2784 Dihedral : 3.227 10.498 2232 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.73 % Allowed : 18.66 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.98 (0.17), residues: 2028 helix: 3.16 (0.12), residues: 1404 sheet: 0.98 (0.45), residues: 132 loop : -1.53 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 133 HIS 0.006 0.001 HIS I 97 PHE 0.010 0.001 PHE H 180 TYR 0.008 0.001 TYR D 65 ARG 0.003 0.000 ARG J 22 Details of bonding type rmsd hydrogen bonds : bond 0.02894 ( 1224) hydrogen bonds : angle 3.17026 ( 3636) SS BOND : bond 0.00149 ( 36) SS BOND : angle 0.63364 ( 72) covalent geometry : bond 0.00262 (17052) covalent geometry : angle 0.47158 (23316) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 311 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8568 (mp) cc_final: 0.8301 (mp) REVERT: A 66 ASP cc_start: 0.9102 (t70) cc_final: 0.8788 (t0) REVERT: A 133 TRP cc_start: 0.7377 (OUTLIER) cc_final: 0.7172 (m-10) REVERT: A 215 ARG cc_start: 0.8681 (tpp-160) cc_final: 0.8114 (tpt170) REVERT: B 66 ASP cc_start: 0.9051 (t70) cc_final: 0.8592 (t0) REVERT: B 93 MET cc_start: 0.9396 (tpp) cc_final: 0.9115 (mtp) REVERT: B 133 TRP cc_start: 0.7391 (OUTLIER) cc_final: 0.7187 (m-10) REVERT: B 169 ASP cc_start: 0.8736 (p0) cc_final: 0.8493 (p0) REVERT: B 215 ARG cc_start: 0.8598 (tpp-160) cc_final: 0.8075 (tpt170) REVERT: C 20 ILE cc_start: 0.8576 (mp) cc_final: 0.8292 (mp) REVERT: C 46 ASP cc_start: 0.8964 (p0) cc_final: 0.8703 (p0) REVERT: C 66 ASP cc_start: 0.9082 (t70) cc_final: 0.8692 (t0) REVERT: C 93 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.8833 (mmm) REVERT: C 133 TRP cc_start: 0.7496 (m-10) cc_final: 0.7276 (m-10) REVERT: C 203 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9102 (mp) REVERT: C 215 ARG cc_start: 0.8622 (tpp-160) cc_final: 0.8193 (tpt170) REVERT: D 66 ASP cc_start: 0.9078 (t70) cc_final: 0.8751 (t0) REVERT: D 133 TRP cc_start: 0.7338 (OUTLIER) cc_final: 0.7108 (m-10) REVERT: D 169 ASP cc_start: 0.8717 (p0) cc_final: 0.8510 (p0) REVERT: D 211 TYR cc_start: 0.8573 (t80) cc_final: 0.8315 (t80) REVERT: D 215 ARG cc_start: 0.8663 (tpp-160) cc_final: 0.8138 (tpt170) REVERT: E 66 ASP cc_start: 0.9057 (t70) cc_final: 0.8592 (t0) REVERT: E 93 MET cc_start: 0.9411 (tpp) cc_final: 0.9133 (mtp) REVERT: E 133 TRP cc_start: 0.7378 (OUTLIER) cc_final: 0.7174 (m-10) REVERT: E 169 ASP cc_start: 0.8776 (p0) cc_final: 0.8544 (p0) REVERT: E 215 ARG cc_start: 0.8568 (tpp-160) cc_final: 0.8073 (tpt170) REVERT: F 20 ILE cc_start: 0.8588 (mp) cc_final: 0.8308 (mp) REVERT: F 46 ASP cc_start: 0.8992 (p0) cc_final: 0.8711 (p0) REVERT: F 66 ASP cc_start: 0.9066 (t70) cc_final: 0.8688 (t0) REVERT: F 93 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.9125 (mmt) REVERT: F 133 TRP cc_start: 0.7430 (OUTLIER) cc_final: 0.7230 (m-10) REVERT: F 203 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9093 (mp) REVERT: F 215 ARG cc_start: 0.8616 (tpp-160) cc_final: 0.8189 (tpt170) REVERT: G 66 ASP cc_start: 0.9094 (t70) cc_final: 0.8767 (t0) REVERT: G 133 TRP cc_start: 0.7339 (OUTLIER) cc_final: 0.7108 (m-10) REVERT: G 211 TYR cc_start: 0.8562 (t80) cc_final: 0.8299 (t80) REVERT: G 215 ARG cc_start: 0.8649 (tpp-160) cc_final: 0.8121 (tpt170) REVERT: H 66 ASP cc_start: 0.9069 (t70) cc_final: 0.8675 (t0) REVERT: H 93 MET cc_start: 0.9434 (tpp) cc_final: 0.9079 (mtp) REVERT: H 133 TRP cc_start: 0.7379 (OUTLIER) cc_final: 0.7177 (m-10) REVERT: H 169 ASP cc_start: 0.8815 (p0) cc_final: 0.8576 (p0) REVERT: H 215 ARG cc_start: 0.8588 (tpp-160) cc_final: 0.8079 (tpt170) REVERT: I 20 ILE cc_start: 0.8621 (mp) cc_final: 0.8328 (mp) REVERT: I 46 ASP cc_start: 0.8946 (p0) cc_final: 0.8697 (p0) REVERT: I 66 ASP cc_start: 0.9091 (t70) cc_final: 0.8705 (t0) REVERT: I 93 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.8841 (mmm) REVERT: I 215 ARG cc_start: 0.8609 (tpp-160) cc_final: 0.8180 (tpt170) REVERT: J 66 ASP cc_start: 0.9117 (t70) cc_final: 0.8792 (t0) REVERT: J 133 TRP cc_start: 0.7356 (OUTLIER) cc_final: 0.7151 (m-10) REVERT: J 211 TYR cc_start: 0.8591 (t80) cc_final: 0.8331 (t80) REVERT: J 215 ARG cc_start: 0.8673 (tpp-160) cc_final: 0.8136 (tpt170) REVERT: K 66 ASP cc_start: 0.9065 (t70) cc_final: 0.8671 (t0) REVERT: K 169 ASP cc_start: 0.8808 (p0) cc_final: 0.8570 (p0) REVERT: K 215 ARG cc_start: 0.8583 (tpp-160) cc_final: 0.8063 (tpt170) REVERT: L 20 ILE cc_start: 0.8614 (mp) cc_final: 0.8325 (mp) REVERT: L 46 ASP cc_start: 0.8951 (p0) cc_final: 0.8682 (p0) REVERT: L 66 ASP cc_start: 0.9101 (t70) cc_final: 0.8715 (t0) REVERT: L 93 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.9085 (mmt) REVERT: L 94 HIS cc_start: 0.8704 (t70) cc_final: 0.8454 (t70) REVERT: L 215 ARG cc_start: 0.8593 (tpp-160) cc_final: 0.8178 (tpt170) outliers start: 88 outliers final: 12 residues processed: 362 average time/residue: 1.1584 time to fit residues: 468.8411 Evaluate side-chains 320 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 294 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 133 TRP Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 133 TRP Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 133 TRP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 114 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 198 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 175 ASN B 54 ASN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN C 54 ASN C 175 ASN D 54 ASN D 97 HIS D 175 ASN E 54 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 ASN F 54 ASN F 97 HIS F 175 ASN G 54 ASN G 97 HIS G 175 ASN H 54 ASN ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN I 54 ASN I 175 ASN J 54 ASN J 175 ASN K 54 ASN K 97 HIS K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.093910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.073145 restraints weight = 31212.739| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.15 r_work: 0.2883 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17088 Z= 0.134 Angle : 0.478 5.229 23388 Z= 0.253 Chirality : 0.042 0.246 2796 Planarity : 0.003 0.022 2784 Dihedral : 3.200 10.566 2232 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 5.32 % Allowed : 18.98 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.02 (0.17), residues: 2028 helix: 3.17 (0.12), residues: 1404 sheet: 1.13 (0.46), residues: 132 loop : -1.50 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 44 HIS 0.002 0.000 HIS B 73 PHE 0.010 0.001 PHE H 180 TYR 0.008 0.001 TYR I 65 ARG 0.003 0.000 ARG I 32 Details of bonding type rmsd hydrogen bonds : bond 0.02848 ( 1224) hydrogen bonds : angle 3.11532 ( 3636) SS BOND : bond 0.00161 ( 36) SS BOND : angle 0.67633 ( 72) covalent geometry : bond 0.00314 (17052) covalent geometry : angle 0.47739 (23316) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 319 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8562 (mp) cc_final: 0.8323 (mp) REVERT: A 66 ASP cc_start: 0.9114 (t70) cc_final: 0.8787 (t0) REVERT: A 133 TRP cc_start: 0.7395 (OUTLIER) cc_final: 0.7193 (m-10) REVERT: A 215 ARG cc_start: 0.8617 (tpp-160) cc_final: 0.8102 (tpt170) REVERT: B 46 ASP cc_start: 0.8863 (p0) cc_final: 0.8658 (p0) REVERT: B 66 ASP cc_start: 0.9082 (t70) cc_final: 0.8611 (t0) REVERT: B 93 MET cc_start: 0.9396 (tpp) cc_final: 0.9086 (mtp) REVERT: B 133 TRP cc_start: 0.7344 (OUTLIER) cc_final: 0.7133 (m-10) REVERT: B 169 ASP cc_start: 0.8759 (p0) cc_final: 0.8510 (p0) REVERT: B 215 ARG cc_start: 0.8597 (tpp-160) cc_final: 0.8059 (tpt170) REVERT: C 20 ILE cc_start: 0.8580 (mp) cc_final: 0.8320 (mp) REVERT: C 46 ASP cc_start: 0.8909 (p0) cc_final: 0.8658 (p0) REVERT: C 66 ASP cc_start: 0.9094 (t70) cc_final: 0.8698 (t0) REVERT: C 93 MET cc_start: 0.9419 (OUTLIER) cc_final: 0.8847 (mmm) REVERT: C 133 TRP cc_start: 0.7426 (m-10) cc_final: 0.7153 (m-10) REVERT: C 203 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9060 (mp) REVERT: C 215 ARG cc_start: 0.8649 (tpp-160) cc_final: 0.8188 (tpt170) REVERT: D 66 ASP cc_start: 0.9092 (t70) cc_final: 0.8750 (t0) REVERT: D 133 TRP cc_start: 0.7317 (OUTLIER) cc_final: 0.7117 (m-10) REVERT: D 211 TYR cc_start: 0.8567 (t80) cc_final: 0.8319 (t80) REVERT: D 215 ARG cc_start: 0.8635 (tpp-160) cc_final: 0.8132 (tpt170) REVERT: E 46 ASP cc_start: 0.8872 (p0) cc_final: 0.8664 (p0) REVERT: E 66 ASP cc_start: 0.9093 (t70) cc_final: 0.8625 (t0) REVERT: E 93 MET cc_start: 0.9411 (tpp) cc_final: 0.9112 (mtp) REVERT: E 133 TRP cc_start: 0.7358 (OUTLIER) cc_final: 0.7148 (m-10) REVERT: E 169 ASP cc_start: 0.8765 (p0) cc_final: 0.8517 (p0) REVERT: E 215 ARG cc_start: 0.8626 (tpp-160) cc_final: 0.8060 (tpt170) REVERT: F 46 ASP cc_start: 0.8936 (p0) cc_final: 0.8682 (p0) REVERT: F 66 ASP cc_start: 0.9084 (t70) cc_final: 0.8696 (t0) REVERT: F 93 MET cc_start: 0.9431 (OUTLIER) cc_final: 0.8827 (mmm) REVERT: F 133 TRP cc_start: 0.7319 (OUTLIER) cc_final: 0.7113 (m-10) REVERT: F 203 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9058 (mp) REVERT: F 215 ARG cc_start: 0.8643 (tpp-160) cc_final: 0.8193 (tpt170) REVERT: G 66 ASP cc_start: 0.9108 (t70) cc_final: 0.8769 (t0) REVERT: G 133 TRP cc_start: 0.7314 (OUTLIER) cc_final: 0.7112 (m-10) REVERT: G 211 TYR cc_start: 0.8545 (t80) cc_final: 0.8302 (t80) REVERT: G 215 ARG cc_start: 0.8634 (tpp-160) cc_final: 0.8130 (tpt170) REVERT: H 46 ASP cc_start: 0.8883 (p0) cc_final: 0.8678 (p0) REVERT: H 66 ASP cc_start: 0.9087 (t70) cc_final: 0.8683 (t0) REVERT: H 80 GLN cc_start: 0.9406 (tt0) cc_final: 0.9204 (tt0) REVERT: H 93 MET cc_start: 0.9437 (tpp) cc_final: 0.9063 (mtp) REVERT: H 133 TRP cc_start: 0.7352 (OUTLIER) cc_final: 0.7146 (m-10) REVERT: H 169 ASP cc_start: 0.8777 (p0) cc_final: 0.8540 (p0) REVERT: H 215 ARG cc_start: 0.8621 (tpp-160) cc_final: 0.8080 (tpt170) REVERT: I 20 ILE cc_start: 0.8607 (mp) cc_final: 0.8341 (mp) REVERT: I 66 ASP cc_start: 0.9111 (t70) cc_final: 0.8718 (t0) REVERT: I 93 MET cc_start: 0.9428 (OUTLIER) cc_final: 0.8861 (mmm) REVERT: I 215 ARG cc_start: 0.8652 (tpp-160) cc_final: 0.8183 (tpt170) REVERT: J 66 ASP cc_start: 0.9117 (t70) cc_final: 0.8782 (t0) REVERT: J 133 TRP cc_start: 0.7349 (OUTLIER) cc_final: 0.7139 (m-10) REVERT: J 211 TYR cc_start: 0.8555 (t80) cc_final: 0.8312 (t80) REVERT: J 215 ARG cc_start: 0.8620 (tpp-160) cc_final: 0.8127 (tpt170) REVERT: K 46 ASP cc_start: 0.8883 (p0) cc_final: 0.8670 (p0) REVERT: K 66 ASP cc_start: 0.9094 (t70) cc_final: 0.8690 (t0) REVERT: K 169 ASP cc_start: 0.8750 (p0) cc_final: 0.8513 (p0) REVERT: K 215 ARG cc_start: 0.8630 (tpp-160) cc_final: 0.8068 (tpt170) REVERT: L 20 ILE cc_start: 0.8601 (mp) cc_final: 0.8330 (mp) REVERT: L 66 ASP cc_start: 0.9112 (t70) cc_final: 0.8717 (t0) REVERT: L 93 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.9128 (mmt) REVERT: L 94 HIS cc_start: 0.8701 (t70) cc_final: 0.8453 (t70) REVERT: L 215 ARG cc_start: 0.8610 (tpp-160) cc_final: 0.8186 (tpt170) outliers start: 99 outliers final: 19 residues processed: 384 average time/residue: 1.1137 time to fit residues: 480.4885 Evaluate side-chains 320 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 287 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 133 TRP Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 133 TRP Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 214 ILE Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 133 TRP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 97 HIS Chi-restraints excluded: chain L residue 214 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 140 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 193 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 13 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 175 ASN A 205 ASN B 97 HIS B 175 ASN C 54 ASN C 175 ASN D 54 ASN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN E 97 HIS E 175 ASN F 54 ASN F 97 HIS F 175 ASN G 54 ASN ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 ASN H 97 HIS H 175 ASN I 54 ASN I 175 ASN J 54 ASN J 175 ASN K 97 HIS K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.095988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074982 restraints weight = 31058.432| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.19 r_work: 0.2947 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17088 Z= 0.110 Angle : 0.480 5.147 23388 Z= 0.256 Chirality : 0.042 0.236 2796 Planarity : 0.003 0.028 2784 Dihedral : 3.183 10.805 2232 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.57 % Allowed : 20.38 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.07 (0.17), residues: 2028 helix: 3.22 (0.12), residues: 1404 sheet: 1.19 (0.47), residues: 132 loop : -1.52 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 133 HIS 0.001 0.000 HIS H 97 PHE 0.010 0.001 PHE H 180 TYR 0.007 0.001 TYR L 65 ARG 0.004 0.001 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.02760 ( 1224) hydrogen bonds : angle 3.07702 ( 3636) SS BOND : bond 0.00155 ( 36) SS BOND : angle 0.58220 ( 72) covalent geometry : bond 0.00246 (17052) covalent geometry : angle 0.47967 (23316) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 316 time to evaluate : 2.075 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: A 20 ILE cc_start: 0.8562 (mp) cc_final: 0.8331 (mp) REVERT: A 66 ASP cc_start: 0.9091 (t70) cc_final: 0.8766 (t0) REVERT: A 215 ARG cc_start: 0.8672 (tpp-160) cc_final: 0.8117 (tpt170) REVERT: B 46 ASP cc_start: 0.8864 (p0) cc_final: 0.8662 (p0) REVERT: B 66 ASP cc_start: 0.9051 (t70) cc_final: 0.8587 (t0) REVERT: B 93 MET cc_start: 0.9406 (tpp) cc_final: 0.9070 (mtp) REVERT: B 133 TRP cc_start: 0.7291 (OUTLIER) cc_final: 0.7090 (m-10) REVERT: B 169 ASP cc_start: 0.8657 (p0) cc_final: 0.8453 (p0) REVERT: B 215 ARG cc_start: 0.8638 (tpp-160) cc_final: 0.8090 (tpt170) REVERT: C 20 ILE cc_start: 0.8549 (mp) cc_final: 0.8294 (mp) REVERT: C 66 ASP cc_start: 0.9104 (t70) cc_final: 0.8730 (t0) REVERT: C 93 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.8829 (mmm) REVERT: C 133 TRP cc_start: 0.7411 (m-10) cc_final: 0.7155 (m-10) REVERT: C 203 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9072 (mp) REVERT: C 215 ARG cc_start: 0.8624 (tpp-160) cc_final: 0.8193 (tpt170) REVERT: D 66 ASP cc_start: 0.9073 (t70) cc_final: 0.8737 (t0) REVERT: D 133 TRP cc_start: 0.7268 (OUTLIER) cc_final: 0.7067 (m-10) REVERT: D 211 TYR cc_start: 0.8555 (t80) cc_final: 0.8300 (t80) REVERT: D 215 ARG cc_start: 0.8707 (tpp-160) cc_final: 0.8154 (tpt170) REVERT: E 66 ASP cc_start: 0.9064 (t70) cc_final: 0.8601 (t0) REVERT: E 93 MET cc_start: 0.9418 (tpp) cc_final: 0.9088 (mtp) REVERT: E 133 TRP cc_start: 0.7275 (OUTLIER) cc_final: 0.7070 (m-10) REVERT: E 215 ARG cc_start: 0.8639 (tpp-160) cc_final: 0.8092 (tpt170) REVERT: F 66 ASP cc_start: 0.9072 (t70) cc_final: 0.8700 (t0) REVERT: F 93 MET cc_start: 0.9406 (OUTLIER) cc_final: 0.8767 (mmm) REVERT: F 203 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9062 (mp) REVERT: F 215 ARG cc_start: 0.8618 (tpp-160) cc_final: 0.8187 (tpt170) REVERT: G 66 ASP cc_start: 0.9097 (t70) cc_final: 0.8766 (t0) REVERT: G 133 TRP cc_start: 0.7251 (OUTLIER) cc_final: 0.7050 (m-10) REVERT: G 211 TYR cc_start: 0.8549 (t80) cc_final: 0.8285 (t80) REVERT: G 215 ARG cc_start: 0.8703 (tpp-160) cc_final: 0.8157 (tpt170) REVERT: H 46 ASP cc_start: 0.8859 (p0) cc_final: 0.8654 (p0) REVERT: H 66 ASP cc_start: 0.9073 (t70) cc_final: 0.8606 (t0) REVERT: H 80 GLN cc_start: 0.9349 (tt0) cc_final: 0.9145 (tt0) REVERT: H 93 MET cc_start: 0.9442 (tpp) cc_final: 0.9060 (mtp) REVERT: H 215 ARG cc_start: 0.8652 (tpp-160) cc_final: 0.8098 (tpt170) REVERT: I 20 ILE cc_start: 0.8585 (mp) cc_final: 0.8349 (mp) REVERT: I 66 ASP cc_start: 0.9102 (t70) cc_final: 0.8728 (t0) REVERT: I 93 MET cc_start: 0.9399 (OUTLIER) cc_final: 0.8826 (mmm) REVERT: I 215 ARG cc_start: 0.8612 (tpp-160) cc_final: 0.8172 (tpt170) REVERT: J 66 ASP cc_start: 0.9104 (t70) cc_final: 0.8775 (t0) REVERT: J 211 TYR cc_start: 0.8576 (t80) cc_final: 0.8320 (t80) REVERT: J 215 ARG cc_start: 0.8706 (tpp-160) cc_final: 0.8160 (tpt170) REVERT: K 66 ASP cc_start: 0.9078 (t70) cc_final: 0.8613 (t0) REVERT: K 215 ARG cc_start: 0.8635 (tpp-160) cc_final: 0.8091 (tpt170) REVERT: L 20 ILE cc_start: 0.8586 (mp) cc_final: 0.8348 (mp) REVERT: L 66 ASP cc_start: 0.9104 (t70) cc_final: 0.8733 (t0) REVERT: L 93 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9111 (mmt) REVERT: L 133 TRP cc_start: 0.7445 (m-10) cc_final: 0.7142 (m-10) REVERT: L 215 ARG cc_start: 0.8619 (tpp-160) cc_final: 0.8176 (tpt170) outliers start: 85 outliers final: 19 residues processed: 364 average time/residue: 1.1178 time to fit residues: 456.1470 Evaluate side-chains 320 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 291 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 60 CYS Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 60 CYS Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 60 CYS Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 134 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 128 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 175 ASN B 80 GLN B 97 HIS B 175 ASN C 54 ASN C 175 ASN D 54 ASN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 205 ASN E 80 GLN E 97 HIS E 175 ASN F 54 ASN F 97 HIS F 175 ASN G 54 ASN ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 ASN G 205 ASN H 54 ASN H 97 HIS H 175 ASN I 54 ASN I 175 ASN J 54 ASN J 175 ASN J 205 ASN K 54 ASN K 97 HIS K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.074394 restraints weight = 31062.580| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.21 r_work: 0.2932 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17088 Z= 0.135 Angle : 0.511 5.758 23388 Z= 0.275 Chirality : 0.042 0.199 2796 Planarity : 0.003 0.025 2784 Dihedral : 3.191 10.898 2232 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.19 % Allowed : 20.59 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.08 (0.17), residues: 2028 helix: 3.18 (0.12), residues: 1404 sheet: 1.25 (0.47), residues: 132 loop : -1.40 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 44 HIS 0.010 0.001 HIS L 94 PHE 0.009 0.001 PHE F 68 TYR 0.008 0.001 TYR D 65 ARG 0.005 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.02779 ( 1224) hydrogen bonds : angle 3.09278 ( 3636) SS BOND : bond 0.00147 ( 36) SS BOND : angle 0.61278 ( 72) covalent geometry : bond 0.00313 (17052) covalent geometry : angle 0.51052 (23316) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 296 time to evaluate : 1.760 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: A 20 ILE cc_start: 0.8572 (mp) cc_final: 0.8361 (mp) REVERT: A 66 ASP cc_start: 0.9101 (t70) cc_final: 0.8784 (t0) REVERT: A 215 ARG cc_start: 0.8641 (tpp-160) cc_final: 0.8125 (tpt170) REVERT: B 46 ASP cc_start: 0.8875 (p0) cc_final: 0.8673 (p0) REVERT: B 66 ASP cc_start: 0.9072 (t70) cc_final: 0.8610 (t0) REVERT: B 93 MET cc_start: 0.9425 (tpp) cc_final: 0.9113 (mtp) REVERT: B 133 TRP cc_start: 0.7268 (OUTLIER) cc_final: 0.7065 (m-10) REVERT: B 169 ASP cc_start: 0.8653 (p0) cc_final: 0.8436 (p0) REVERT: B 215 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8087 (tpt170) REVERT: C 20 ILE cc_start: 0.8558 (mp) cc_final: 0.8331 (mp) REVERT: C 93 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.8826 (mmm) REVERT: C 133 TRP cc_start: 0.7389 (m-10) cc_final: 0.7131 (m-10) REVERT: C 203 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9106 (mp) REVERT: C 215 ARG cc_start: 0.8578 (tpp-160) cc_final: 0.8189 (tpt170) REVERT: D 66 ASP cc_start: 0.9073 (t70) cc_final: 0.8753 (t0) REVERT: D 133 TRP cc_start: 0.7250 (OUTLIER) cc_final: 0.7047 (m-10) REVERT: D 211 TYR cc_start: 0.8579 (t80) cc_final: 0.8320 (t80) REVERT: D 215 ARG cc_start: 0.8685 (tpp-160) cc_final: 0.8164 (tpt170) REVERT: E 66 ASP cc_start: 0.9087 (t70) cc_final: 0.8623 (t0) REVERT: E 93 MET cc_start: 0.9432 (tpp) cc_final: 0.9126 (mtp) REVERT: E 215 ARG cc_start: 0.8617 (tpp-160) cc_final: 0.8092 (tpt170) REVERT: F 20 ILE cc_start: 0.8570 (mp) cc_final: 0.8343 (mp) REVERT: F 93 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.8887 (mmm) REVERT: F 133 TRP cc_start: 0.7369 (m-10) cc_final: 0.7118 (m-10) REVERT: F 203 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.9099 (mp) REVERT: F 215 ARG cc_start: 0.8559 (tpp-160) cc_final: 0.8188 (tpt170) REVERT: G 66 ASP cc_start: 0.9098 (t70) cc_final: 0.8784 (t0) REVERT: G 133 TRP cc_start: 0.7235 (OUTLIER) cc_final: 0.7031 (m-10) REVERT: G 211 TYR cc_start: 0.8576 (t80) cc_final: 0.8312 (t80) REVERT: G 215 ARG cc_start: 0.8654 (tpp-160) cc_final: 0.8157 (tpt170) REVERT: H 46 ASP cc_start: 0.8878 (p0) cc_final: 0.8672 (p0) REVERT: H 66 ASP cc_start: 0.9099 (t70) cc_final: 0.8635 (t0) REVERT: H 93 MET cc_start: 0.9445 (tpp) cc_final: 0.9046 (mtp) REVERT: H 215 ARG cc_start: 0.8630 (tpp-160) cc_final: 0.8087 (tpt170) REVERT: I 20 ILE cc_start: 0.8596 (mp) cc_final: 0.8363 (mp) REVERT: I 93 MET cc_start: 0.9395 (OUTLIER) cc_final: 0.8813 (mmm) REVERT: I 215 ARG cc_start: 0.8561 (tpp-160) cc_final: 0.8177 (tpt170) REVERT: J 66 ASP cc_start: 0.9105 (t70) cc_final: 0.8794 (t0) REVERT: J 211 TYR cc_start: 0.8588 (t80) cc_final: 0.8327 (t80) REVERT: J 215 ARG cc_start: 0.8674 (tpp-160) cc_final: 0.8159 (tpt170) REVERT: K 66 ASP cc_start: 0.9094 (t70) cc_final: 0.8631 (t0) REVERT: K 93 MET cc_start: 0.9435 (tpp) cc_final: 0.9225 (mmt) REVERT: K 215 ARG cc_start: 0.8610 (tpp-160) cc_final: 0.8084 (tpt170) REVERT: L 20 ILE cc_start: 0.8592 (mp) cc_final: 0.8357 (mp) REVERT: L 93 MET cc_start: 0.9404 (OUTLIER) cc_final: 0.9115 (mmt) REVERT: L 133 TRP cc_start: 0.7419 (m-10) cc_final: 0.7075 (m-10) REVERT: L 215 ARG cc_start: 0.8584 (tpp-160) cc_final: 0.8190 (tpt170) outliers start: 78 outliers final: 28 residues processed: 346 average time/residue: 1.1063 time to fit residues: 429.8102 Evaluate side-chains 322 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 60 CYS Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 60 CYS Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 214 ILE Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 60 CYS Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 214 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 110 optimal weight: 0.0570 chunk 7 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 181 optimal weight: 0.0040 chunk 56 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.5710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 175 ASN B 97 HIS B 175 ASN C 54 ASN C 175 ASN D 54 ASN D 97 HIS D 175 ASN E 97 HIS E 175 ASN F 54 ASN F 97 HIS F 175 ASN G 54 ASN G 97 HIS G 175 ASN H 97 HIS H 175 ASN I 54 ASN I 175 ASN J 54 ASN J 175 ASN K 97 HIS K 175 ASN L 54 ASN L 97 HIS L 175 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.096673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.075809 restraints weight = 31074.662| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.21 r_work: 0.2964 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17088 Z= 0.119 Angle : 0.508 6.693 23388 Z= 0.274 Chirality : 0.041 0.167 2796 Planarity : 0.003 0.028 2784 Dihedral : 3.187 11.197 2232 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.87 % Allowed : 21.08 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.11 (0.17), residues: 2028 helix: 3.20 (0.12), residues: 1404 sheet: 1.24 (0.48), residues: 132 loop : -1.33 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 44 HIS 0.002 0.000 HIS C 97 PHE 0.009 0.001 PHE K 180 TYR 0.008 0.001 TYR E 171 ARG 0.005 0.001 ARG K 32 Details of bonding type rmsd hydrogen bonds : bond 0.02707 ( 1224) hydrogen bonds : angle 3.06610 ( 3636) SS BOND : bond 0.00138 ( 36) SS BOND : angle 0.51721 ( 72) covalent geometry : bond 0.00270 (17052) covalent geometry : angle 0.50786 (23316) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 308 time to evaluate : 1.969 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 66 ASP cc_start: 0.9070 (t70) cc_final: 0.8743 (t0) REVERT: A 215 ARG cc_start: 0.8630 (tpp-160) cc_final: 0.8108 (tpt170) REVERT: B 46 ASP cc_start: 0.8858 (p0) cc_final: 0.8642 (p0) REVERT: B 66 ASP cc_start: 0.9049 (t70) cc_final: 0.8593 (t0) REVERT: B 93 MET cc_start: 0.9426 (tpp) cc_final: 0.9121 (mtp) REVERT: B 215 ARG cc_start: 0.8646 (tpp-160) cc_final: 0.8104 (tpt170) REVERT: C 20 ILE cc_start: 0.8492 (mp) cc_final: 0.8282 (mp) REVERT: C 89 LEU cc_start: 0.9295 (tp) cc_final: 0.9084 (tt) REVERT: C 93 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.8775 (mmm) REVERT: C 133 TRP cc_start: 0.7349 (m-10) cc_final: 0.7035 (m-10) REVERT: C 203 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9093 (mp) REVERT: C 215 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8183 (tpt170) REVERT: D 66 ASP cc_start: 0.9053 (t70) cc_final: 0.8721 (t0) REVERT: D 211 TYR cc_start: 0.8565 (t80) cc_final: 0.8298 (t80) REVERT: D 215 ARG cc_start: 0.8685 (tpp-160) cc_final: 0.8151 (tpt170) REVERT: E 66 ASP cc_start: 0.9049 (t70) cc_final: 0.8590 (t0) REVERT: E 93 MET cc_start: 0.9425 (tpp) cc_final: 0.9119 (mtp) REVERT: E 215 ARG cc_start: 0.8637 (tpp-160) cc_final: 0.8110 (tpt170) REVERT: F 20 ILE cc_start: 0.8542 (mp) cc_final: 0.8299 (mp) REVERT: F 133 TRP cc_start: 0.7307 (m-10) cc_final: 0.7068 (m-10) REVERT: F 203 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9090 (mp) REVERT: F 215 ARG cc_start: 0.8583 (tpp-160) cc_final: 0.8186 (tpt170) REVERT: G 66 ASP cc_start: 0.9068 (t70) cc_final: 0.8740 (t0) REVERT: G 211 TYR cc_start: 0.8570 (t80) cc_final: 0.8300 (t80) REVERT: G 215 ARG cc_start: 0.8663 (tpp-160) cc_final: 0.8141 (tpt170) REVERT: H 46 ASP cc_start: 0.8851 (p0) cc_final: 0.8630 (p0) REVERT: H 66 ASP cc_start: 0.9059 (t70) cc_final: 0.8591 (t0) REVERT: H 93 MET cc_start: 0.9438 (tpp) cc_final: 0.9035 (mtp) REVERT: H 215 ARG cc_start: 0.8658 (tpp-160) cc_final: 0.8089 (tpt170) REVERT: I 20 ILE cc_start: 0.8561 (mp) cc_final: 0.8340 (mp) REVERT: I 89 LEU cc_start: 0.9292 (tp) cc_final: 0.9090 (tt) REVERT: I 93 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.8773 (mmm) REVERT: I 133 TRP cc_start: 0.7300 (m-10) cc_final: 0.7051 (m-10) REVERT: I 215 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8176 (tpt170) REVERT: J 66 ASP cc_start: 0.9065 (t70) cc_final: 0.8739 (t0) REVERT: J 211 TYR cc_start: 0.8569 (t80) cc_final: 0.8304 (t80) REVERT: J 215 ARG cc_start: 0.8675 (tpp-160) cc_final: 0.8137 (tpt170) REVERT: K 66 ASP cc_start: 0.9058 (t70) cc_final: 0.8589 (t0) REVERT: K 93 MET cc_start: 0.9422 (tpp) cc_final: 0.9209 (mmt) REVERT: K 133 TRP cc_start: 0.7270 (m-10) cc_final: 0.7043 (m-10) REVERT: K 215 ARG cc_start: 0.8651 (tpp-160) cc_final: 0.8108 (tpt170) REVERT: L 20 ILE cc_start: 0.8544 (mp) cc_final: 0.8316 (mp) REVERT: L 93 MET cc_start: 0.9399 (OUTLIER) cc_final: 0.9122 (mmt) REVERT: L 133 TRP cc_start: 0.7345 (m-10) cc_final: 0.7007 (m-10) REVERT: L 215 ARG cc_start: 0.8589 (tpp-160) cc_final: 0.8171 (tpt170) outliers start: 72 outliers final: 21 residues processed: 353 average time/residue: 1.0831 time to fit residues: 431.4328 Evaluate side-chains 321 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 295 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain F residue 60 CYS Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 60 CYS Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 214 ILE Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 60 CYS Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 214 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 36 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 195 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 175 ASN B 54 ASN B 97 HIS B 175 ASN C 54 ASN C 175 ASN D 54 ASN D 97 HIS D 175 ASN E 54 ASN E 97 HIS E 175 ASN F 54 ASN F 97 HIS F 175 ASN G 54 ASN G 97 HIS G 175 ASN H 97 HIS H 175 ASN I 54 ASN I 175 ASN J 54 ASN J 175 ASN ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.096137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075122 restraints weight = 31190.516| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.21 r_work: 0.2957 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17088 Z= 0.132 Angle : 0.519 6.899 23388 Z= 0.280 Chirality : 0.041 0.154 2796 Planarity : 0.003 0.027 2784 Dihedral : 3.175 11.059 2232 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.90 % Allowed : 22.31 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.18 (0.17), residues: 2028 helix: 3.21 (0.12), residues: 1404 sheet: 1.40 (0.48), residues: 132 loop : -1.21 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 133 HIS 0.002 0.000 HIS I 97 PHE 0.008 0.001 PHE I 180 TYR 0.008 0.001 TYR B 65 ARG 0.005 0.001 ARG H 32 Details of bonding type rmsd hydrogen bonds : bond 0.02709 ( 1224) hydrogen bonds : angle 3.05094 ( 3636) SS BOND : bond 0.00141 ( 36) SS BOND : angle 0.58576 ( 72) covalent geometry : bond 0.00305 (17052) covalent geometry : angle 0.51897 (23316) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 308 time to evaluate : 1.782 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 66 ASP cc_start: 0.9090 (t70) cc_final: 0.8762 (t0) REVERT: A 215 ARG cc_start: 0.8656 (tpp-160) cc_final: 0.8122 (tpt170) REVERT: B 46 ASP cc_start: 0.8839 (p0) cc_final: 0.8608 (p0) REVERT: B 54 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8838 (t0) REVERT: B 66 ASP cc_start: 0.9066 (t70) cc_final: 0.8610 (t0) REVERT: B 93 MET cc_start: 0.9419 (tpp) cc_final: 0.9101 (mtp) REVERT: B 215 ARG cc_start: 0.8657 (tpp-160) cc_final: 0.8117 (tpt170) REVERT: C 20 ILE cc_start: 0.8467 (mp) cc_final: 0.8265 (mp) REVERT: C 93 MET cc_start: 0.9398 (OUTLIER) cc_final: 0.9054 (mmm) REVERT: C 94 HIS cc_start: 0.8878 (t-90) cc_final: 0.8596 (t70) REVERT: C 203 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9092 (mp) REVERT: C 215 ARG cc_start: 0.8584 (tpp-160) cc_final: 0.8175 (tpt170) REVERT: D 66 ASP cc_start: 0.9060 (t70) cc_final: 0.8727 (t0) REVERT: D 211 TYR cc_start: 0.8581 (t80) cc_final: 0.8305 (t80) REVERT: D 215 ARG cc_start: 0.8686 (tpp-160) cc_final: 0.8138 (tpt170) REVERT: E 54 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8870 (t0) REVERT: E 66 ASP cc_start: 0.9070 (t70) cc_final: 0.8613 (t0) REVERT: E 93 MET cc_start: 0.9429 (tpp) cc_final: 0.9118 (mtp) REVERT: E 215 ARG cc_start: 0.8658 (tpp-160) cc_final: 0.8122 (tpt170) REVERT: F 20 ILE cc_start: 0.8534 (mp) cc_final: 0.8305 (mp) REVERT: F 203 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9084 (mp) REVERT: F 211 TYR cc_start: 0.8624 (t80) cc_final: 0.8187 (t80) REVERT: F 215 ARG cc_start: 0.8596 (tpp-160) cc_final: 0.8305 (tpt170) REVERT: G 66 ASP cc_start: 0.9091 (t70) cc_final: 0.8767 (t0) REVERT: G 211 TYR cc_start: 0.8567 (t80) cc_final: 0.8290 (t80) REVERT: G 215 ARG cc_start: 0.8655 (tpp-160) cc_final: 0.8120 (tpt170) REVERT: H 46 ASP cc_start: 0.8858 (p0) cc_final: 0.8625 (p0) REVERT: H 66 ASP cc_start: 0.9070 (t70) cc_final: 0.8610 (t0) REVERT: H 93 MET cc_start: 0.9438 (tpp) cc_final: 0.9020 (mtp) REVERT: H 215 ARG cc_start: 0.8664 (tpp-160) cc_final: 0.8097 (tpt170) REVERT: I 20 ILE cc_start: 0.8546 (mp) cc_final: 0.8335 (mp) REVERT: I 93 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.9048 (mmm) REVERT: I 94 HIS cc_start: 0.8874 (t-90) cc_final: 0.8594 (t70) REVERT: I 211 TYR cc_start: 0.8621 (t80) cc_final: 0.8188 (t80) REVERT: I 215 ARG cc_start: 0.8591 (tpp-160) cc_final: 0.8290 (tpt170) REVERT: J 66 ASP cc_start: 0.9080 (t70) cc_final: 0.8754 (t0) REVERT: J 211 TYR cc_start: 0.8583 (t80) cc_final: 0.8304 (t80) REVERT: J 215 ARG cc_start: 0.8643 (tpp-160) cc_final: 0.8117 (tpt170) REVERT: K 66 ASP cc_start: 0.9081 (t70) cc_final: 0.8624 (t0) REVERT: K 93 MET cc_start: 0.9430 (tpp) cc_final: 0.9216 (mmt) REVERT: K 215 ARG cc_start: 0.8662 (tpp-160) cc_final: 0.8117 (tpt170) REVERT: L 93 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.9098 (mmt) REVERT: L 211 TYR cc_start: 0.8632 (t80) cc_final: 0.8204 (t80) REVERT: L 215 ARG cc_start: 0.8577 (tpp-160) cc_final: 0.8284 (tpt170) outliers start: 54 outliers final: 18 residues processed: 350 average time/residue: 1.0653 time to fit residues: 420.2059 Evaluate side-chains 322 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 297 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain F residue 60 CYS Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 60 CYS Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 60 CYS Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 134 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 113 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 141 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 chunk 183 optimal weight: 0.0000 chunk 105 optimal weight: 0.1980 chunk 192 optimal weight: 0.6980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 175 ASN B 54 ASN B 97 HIS B 175 ASN C 54 ASN C 99 GLN C 175 ASN D 54 ASN D 97 HIS D 175 ASN E 54 ASN E 97 HIS E 175 ASN F 54 ASN F 97 HIS F 175 ASN G 54 ASN G 97 HIS G 175 ASN H 97 HIS H 175 ASN I 54 ASN I 175 ASN J 54 ASN J 97 HIS J 175 ASN K 97 HIS K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.096840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.075946 restraints weight = 30983.142| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.18 r_work: 0.2971 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17088 Z= 0.123 Angle : 0.527 7.229 23388 Z= 0.284 Chirality : 0.040 0.171 2796 Planarity : 0.003 0.029 2784 Dihedral : 3.202 11.552 2232 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.44 % Allowed : 21.51 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.17 (0.17), residues: 2028 helix: 3.19 (0.12), residues: 1404 sheet: 1.38 (0.47), residues: 132 loop : -1.16 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 133 HIS 0.009 0.001 HIS L 94 PHE 0.008 0.001 PHE K 180 TYR 0.007 0.001 TYR C 65 ARG 0.005 0.001 ARG H 32 Details of bonding type rmsd hydrogen bonds : bond 0.02679 ( 1224) hydrogen bonds : angle 3.04803 ( 3636) SS BOND : bond 0.00132 ( 36) SS BOND : angle 0.61097 ( 72) covalent geometry : bond 0.00276 (17052) covalent geometry : angle 0.52692 (23316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11198.48 seconds wall clock time: 193 minutes 39.68 seconds (11619.68 seconds total)