Starting phenix.real_space_refine on Sat Jun 14 16:59:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qjh_18447/06_2025/8qjh_18447_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qjh_18447/06_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_18447/06_2025/8qjh_18447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qjh_18447/06_2025/8qjh_18447.map" model { file = "/net/cci-nas-00/data/ceres_data/8qjh_18447/06_2025/8qjh_18447_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qjh_18447/06_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-5710/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: 5.30, 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: 3.74 Conformation dependent library (CDL) restraints added in 2.2 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: 1.40 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: 4.75 Time building geometry restraints manager: 4.49 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: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 31.420 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.340 ------------------------------------------------------------------------------- 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 : 1.982 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: 1.1778 time to fit residues: 653.9976 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 : 1.890 ------------------------------------------------------------------------------- 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 = 0.094587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.073250 restraints weight = 30957.141| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.14 r_work: 0.2919 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17088 Z= 0.188 Angle : 0.547 5.504 23388 Z= 0.288 Chirality : 0.044 0.203 2796 Planarity : 0.003 0.017 2784 Dihedral : 3.315 11.208 2232 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.57 % Allowed : 13.71 % Favored : 81.72 % 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: 1.32 (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 L 73 PHE 0.011 0.002 PHE G 190 TYR 0.014 0.001 TYR F 211 ARG 0.004 0.001 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 1224) hydrogen bonds : angle 3.52430 ( 3636) SS BOND : bond 0.00137 ( 36) SS BOND : angle 1.17410 ( 72) covalent geometry : bond 0.00442 (17052) covalent geometry : angle 0.54352 (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 404 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 319 time to evaluate : 1.601 Fit side-chains REVERT: A 66 ASP cc_start: 0.9095 (t70) cc_final: 0.8761 (t0) REVERT: A 133 TRP cc_start: 0.7527 (OUTLIER) cc_final: 0.7283 (m-10) REVERT: A 169 ASP cc_start: 0.8721 (p0) cc_final: 0.8508 (p0) REVERT: A 215 ARG cc_start: 0.8740 (tpp-160) cc_final: 0.8097 (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: 0.7484 (OUTLIER) cc_final: 0.7234 (m-10) REVERT: B 162 MET cc_start: 0.9078 (mmt) cc_final: 0.8868 (mmt) REVERT: B 169 ASP cc_start: 0.8868 (p0) cc_final: 0.8614 (p0) REVERT: B 215 ARG cc_start: 0.8604 (tpp-160) cc_final: 0.8055 (tpt170) REVERT: C 46 ASP cc_start: 0.8967 (p0) cc_final: 0.8708 (p0) REVERT: C 47 GLU cc_start: 0.8808 (pt0) cc_final: 0.8588 (pt0) REVERT: C 66 ASP cc_start: 0.9070 (t70) cc_final: 0.8696 (t0) REVERT: C 93 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8938 (mmm) REVERT: C 133 TRP cc_start: 0.7538 (OUTLIER) cc_final: 0.7333 (m-10) REVERT: C 203 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9171 (mp) REVERT: C 215 ARG cc_start: 0.8629 (tpp-160) cc_final: 0.8166 (tpt170) REVERT: D 66 ASP cc_start: 0.9076 (t70) cc_final: 0.8747 (t0) REVERT: D 133 TRP cc_start: 0.7490 (OUTLIER) cc_final: 0.7222 (m-10) REVERT: D 169 ASP cc_start: 0.8732 (p0) cc_final: 0.8528 (p0) REVERT: D 211 TYR cc_start: 0.8607 (t80) cc_final: 0.8383 (t80) REVERT: D 215 ARG cc_start: 0.8660 (tpp-160) cc_final: 0.8116 (tpt170) REVERT: E 47 GLU cc_start: 0.8776 (pt0) cc_final: 0.8524 (pt0) REVERT: E 66 ASP cc_start: 0.9037 (t70) cc_final: 0.8584 (t0) REVERT: E 133 TRP cc_start: 0.7486 (OUTLIER) cc_final: 0.7240 (m-10) REVERT: E 162 MET cc_start: 0.9076 (mmt) cc_final: 0.8869 (mmt) REVERT: E 169 ASP cc_start: 0.8887 (p0) cc_final: 0.8641 (p0) REVERT: E 215 ARG cc_start: 0.8609 (tpp-160) cc_final: 0.8068 (tpt170) REVERT: F 46 ASP cc_start: 0.8962 (p0) cc_final: 0.8694 (p0) REVERT: F 47 GLU cc_start: 0.8799 (pt0) cc_final: 0.8559 (pt0) REVERT: F 66 ASP cc_start: 0.9074 (t70) cc_final: 0.8703 (t0) REVERT: F 93 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.8798 (mmm) REVERT: F 133 TRP cc_start: 0.7502 (OUTLIER) cc_final: 0.7296 (m-10) REVERT: F 203 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9165 (mp) REVERT: F 215 ARG cc_start: 0.8637 (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: 0.8704 (p0) cc_final: 0.8491 (p0) REVERT: G 211 TYR cc_start: 0.8597 (t80) cc_final: 0.8371 (t80) REVERT: G 215 ARG cc_start: 0.8672 (tpp-160) cc_final: 0.8123 (tpt170) REVERT: H 47 GLU cc_start: 0.8785 (pt0) cc_final: 0.8534 (pt0) REVERT: H 66 ASP cc_start: 0.9044 (t70) cc_final: 0.8588 (t0) REVERT: H 133 TRP cc_start: 0.7508 (OUTLIER) cc_final: 0.7245 (m-10) REVERT: H 169 ASP cc_start: 0.8900 (p0) cc_final: 0.8650 (p0) REVERT: H 215 ARG cc_start: 0.8634 (tpp-160) cc_final: 0.8055 (tpt170) REVERT: I 46 ASP cc_start: 0.8958 (p0) cc_final: 0.8718 (p0) REVERT: I 47 GLU cc_start: 0.8818 (pt0) cc_final: 0.8605 (pt0) REVERT: I 66 ASP cc_start: 0.9087 (t70) cc_final: 0.8722 (t0) REVERT: I 93 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8951 (mmm) REVERT: I 133 TRP cc_start: 0.7514 (OUTLIER) cc_final: 0.7305 (m-10) REVERT: I 215 ARG cc_start: 0.8592 (tpp-160) cc_final: 0.8145 (tpt170) REVERT: J 66 ASP cc_start: 0.9085 (t70) cc_final: 0.8752 (t0) REVERT: J 133 TRP cc_start: 0.7493 (OUTLIER) cc_final: 0.7248 (m-10) REVERT: J 169 ASP cc_start: 0.8740 (p0) cc_final: 0.8529 (p0) REVERT: J 211 TYR cc_start: 0.8585 (t80) cc_final: 0.8357 (t80) REVERT: J 215 ARG cc_start: 0.8659 (tpp-160) cc_final: 0.8110 (tpt170) REVERT: K 47 GLU cc_start: 0.8781 (pt0) cc_final: 0.8531 (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: 0.7234 (m-10) REVERT: K 146 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8829 (mm-30) REVERT: K 162 MET cc_start: 0.9068 (mmt) cc_final: 0.8721 (mmt) REVERT: K 169 ASP cc_start: 0.8900 (p0) cc_final: 0.8646 (p0) REVERT: K 215 ARG cc_start: 0.8617 (tpp-160) cc_final: 0.8051 (tpt170) REVERT: L 46 ASP cc_start: 0.8960 (p0) cc_final: 0.8709 (p0) REVERT: L 47 GLU cc_start: 0.8801 (pt0) cc_final: 0.8585 (pt0) REVERT: L 66 ASP cc_start: 0.9089 (t70) cc_final: 0.8721 (t0) REVERT: L 93 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.9053 (mmm) REVERT: L 94 HIS cc_start: 0.8795 (t70) cc_final: 0.8501 (t-90) REVERT: L 215 ARG cc_start: 0.8627 (tpp-160) cc_final: 0.8153 (tpt170) outliers start: 85 outliers final: 21 residues processed: 371 average time/residue: 1.1933 time to fit residues: 493.5941 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 : 1.823 ------------------------------------------------------------------------------- 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: 0.8980 chunk 89 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 192 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.094450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.073696 restraints weight = 31100.747| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.18 r_work: 0.2929 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 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 0.041 17088 Z= 0.127 Angle : 0.491 5.261 23388 Z= 0.262 Chirality : 0.042 0.230 2796 Planarity : 0.003 0.020 2784 Dihedral : 3.292 10.592 2232 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.87 % Allowed : 17.47 % Favored : 78.66 % 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: 0.90 (0.45), residues: 132 loop : -1.57 (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 D 97 PHE 0.009 0.001 PHE A 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 0.03165 ( 1224) hydrogen bonds : angle 3.32562 ( 3636) SS BOND : bond 0.00130 ( 36) SS BOND : angle 0.80896 ( 72) covalent geometry : bond 0.00293 (17052) covalent geometry : angle 0.48945 (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 386 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 314 time to evaluate : 2.079 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.9073 (t70) cc_final: 0.8772 (t0) REVERT: A 93 MET cc_start: 0.9055 (mmt) cc_final: 0.8846 (mmt) REVERT: A 133 TRP cc_start: 0.7484 (OUTLIER) cc_final: 0.7274 (m-10) REVERT: A 215 ARG cc_start: 0.8744 (tpp-160) cc_final: 0.8140 (tpt170) REVERT: B 66 ASP cc_start: 0.9008 (t70) cc_final: 0.8611 (t0) REVERT: B 93 MET cc_start: 0.9347 (tpp) cc_final: 0.9051 (mtp) REVERT: B 133 TRP cc_start: 0.7445 (OUTLIER) cc_final: 0.7200 (m-10) REVERT: B 169 ASP cc_start: 0.8848 (p0) cc_final: 0.8581 (p0) REVERT: B 215 ARG cc_start: 0.8587 (tpp-160) cc_final: 0.8071 (tpt170) REVERT: C 46 ASP cc_start: 0.8994 (p0) cc_final: 0.8708 (p0) REVERT: C 47 GLU cc_start: 0.8754 (pt0) cc_final: 0.8549 (pt0) REVERT: C 66 ASP cc_start: 0.9042 (t70) cc_final: 0.8661 (t0) REVERT: C 93 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.9069 (mmt) REVERT: C 133 TRP cc_start: 0.7517 (OUTLIER) cc_final: 0.7311 (m-10) REVERT: C 203 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9147 (mp) REVERT: C 215 ARG cc_start: 0.8648 (tpp-160) cc_final: 0.8190 (tpt170) REVERT: D 66 ASP cc_start: 0.9039 (t70) cc_final: 0.8737 (t0) REVERT: D 133 TRP cc_start: 0.7408 (OUTLIER) cc_final: 0.7168 (m-10) REVERT: D 169 ASP cc_start: 0.8766 (p0) cc_final: 0.8562 (p0) REVERT: D 211 TYR cc_start: 0.8577 (t80) cc_final: 0.8336 (t80) REVERT: D 215 ARG cc_start: 0.8631 (tpp-160) cc_final: 0.8106 (tpt170) REVERT: E 66 ASP cc_start: 0.9012 (t70) cc_final: 0.8615 (t0) REVERT: E 93 MET cc_start: 0.9370 (tpp) cc_final: 0.9087 (mtp) REVERT: E 133 TRP cc_start: 0.7435 (OUTLIER) cc_final: 0.7189 (m-10) REVERT: E 169 ASP cc_start: 0.8862 (p0) cc_final: 0.8606 (p0) REVERT: E 215 ARG cc_start: 0.8585 (tpp-160) cc_final: 0.8064 (tpt170) REVERT: F 46 ASP cc_start: 0.9000 (p0) cc_final: 0.8712 (p0) REVERT: F 47 GLU cc_start: 0.8767 (pt0) cc_final: 0.8544 (pt0) REVERT: F 66 ASP cc_start: 0.9048 (t70) cc_final: 0.8671 (t0) REVERT: F 93 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.9168 (mmt) REVERT: F 133 TRP cc_start: 0.7485 (OUTLIER) cc_final: 0.7284 (m-10) REVERT: F 203 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9144 (mp) REVERT: F 215 ARG cc_start: 0.8647 (tpp-160) cc_final: 0.8196 (tpt170) REVERT: G 66 ASP cc_start: 0.9035 (t70) cc_final: 0.8728 (t0) REVERT: G 133 TRP cc_start: 0.7421 (OUTLIER) cc_final: 0.7186 (m-10) REVERT: G 169 ASP cc_start: 0.8770 (p0) cc_final: 0.8558 (p0) REVERT: G 211 TYR cc_start: 0.8585 (t80) cc_final: 0.8335 (t80) REVERT: G 215 ARG cc_start: 0.8639 (tpp-160) cc_final: 0.8111 (tpt170) REVERT: H 47 GLU cc_start: 0.8786 (pt0) cc_final: 0.8583 (pt0) REVERT: H 66 ASP cc_start: 0.9030 (t70) cc_final: 0.8574 (t0) REVERT: H 133 TRP cc_start: 0.7458 (OUTLIER) cc_final: 0.7218 (m-10) REVERT: H 169 ASP cc_start: 0.8905 (p0) cc_final: 0.8629 (p0) REVERT: H 215 ARG cc_start: 0.8598 (tpp-160) cc_final: 0.8063 (tpt170) REVERT: I 20 ILE cc_start: 0.8624 (mp) cc_final: 0.8304 (mp) REVERT: I 46 ASP cc_start: 0.8996 (p0) cc_final: 0.8715 (p0) REVERT: I 47 GLU cc_start: 0.8783 (pt0) cc_final: 0.8573 (pt0) REVERT: I 66 ASP cc_start: 0.9048 (t70) cc_final: 0.8669 (t0) REVERT: I 93 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.9140 (mmt) REVERT: I 133 TRP cc_start: 0.7488 (OUTLIER) cc_final: 0.7286 (m-10) REVERT: I 215 ARG cc_start: 0.8644 (tpp-160) cc_final: 0.8174 (tpt170) REVERT: J 66 ASP cc_start: 0.9066 (t70) cc_final: 0.8769 (t0) REVERT: J 133 TRP cc_start: 0.7440 (OUTLIER) cc_final: 0.7229 (m-10) REVERT: J 169 ASP cc_start: 0.8778 (p0) cc_final: 0.8561 (p0) REVERT: J 211 TYR cc_start: 0.8591 (t80) cc_final: 0.8342 (t80) REVERT: J 215 ARG cc_start: 0.8681 (tpp-160) cc_final: 0.8128 (tpt170) REVERT: K 47 GLU cc_start: 0.8799 (pt0) cc_final: 0.8598 (pt0) REVERT: K 66 ASP cc_start: 0.9021 (t70) cc_final: 0.8563 (t0) REVERT: K 133 TRP cc_start: 0.7448 (OUTLIER) cc_final: 0.7209 (m-10) REVERT: K 169 ASP cc_start: 0.8910 (p0) cc_final: 0.8643 (p0) REVERT: K 215 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8060 (tpt170) REVERT: L 20 ILE cc_start: 0.8622 (mp) cc_final: 0.8301 (mp) REVERT: L 46 ASP cc_start: 0.8997 (p0) cc_final: 0.8708 (p0) REVERT: L 47 GLU cc_start: 0.8766 (pt0) cc_final: 0.8559 (pt0) REVERT: L 66 ASP cc_start: 0.9065 (t70) cc_final: 0.8688 (t0) REVERT: L 93 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.9103 (mmt) REVERT: L 94 HIS cc_start: 0.8730 (t70) cc_final: 0.8508 (t70) REVERT: L 215 ARG cc_start: 0.8630 (tpp-160) cc_final: 0.8176 (tpt170) outliers start: 72 outliers final: 15 residues processed: 351 average time/residue: 1.2139 time to fit residues: 476.0972 Evaluate side-chains 318 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 286 time to evaluate : 2.056 ------------------------------------------------------------------------------- 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 71 ILE 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: 0.9990 chunk 202 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 170 optimal weight: 9.9990 chunk 81 optimal weight: 0.0570 chunk 76 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- 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 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 E 175 ASN 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: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.095028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.074259 restraints weight = 31108.501| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.17 r_work: 0.2942 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.2485 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= 0.114 Angle : 0.473 5.217 23388 Z= 0.250 Chirality : 0.042 0.240 2796 Planarity : 0.003 0.021 2784 Dihedral : 3.216 10.500 2232 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.41 % Allowed : 18.12 % Favored : 77.47 % 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: 3.01 (0.17), residues: 2028 helix: 3.21 (0.12), residues: 1404 sheet: 0.96 (0.45), residues: 132 loop : -1.60 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 133 HIS 0.006 0.001 HIS I 97 PHE 0.010 0.001 PHE H 180 TYR 0.007 0.001 TYR G 65 ARG 0.008 0.000 ARG D 22 Details of bonding type rmsd hydrogen bonds : bond 0.02961 ( 1224) hydrogen bonds : angle 3.18946 ( 3636) SS BOND : bond 0.00123 ( 36) SS BOND : angle 0.66882 ( 72) covalent geometry : bond 0.00259 (17052) covalent geometry : angle 0.47188 (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 401 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 319 time to evaluate : 1.780 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8526 (mp) cc_final: 0.8214 (mp) REVERT: A 66 ASP cc_start: 0.9072 (t70) cc_final: 0.8771 (t0) REVERT: A 93 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8837 (mmt) REVERT: A 133 TRP cc_start: 0.7435 (OUTLIER) cc_final: 0.7229 (m-10) REVERT: A 169 ASP cc_start: 0.8704 (p0) cc_final: 0.8494 (p0) REVERT: A 215 ARG cc_start: 0.8706 (tpp-160) cc_final: 0.8137 (tpt170) REVERT: B 66 ASP cc_start: 0.9019 (t70) cc_final: 0.8626 (t0) REVERT: B 93 MET cc_start: 0.9369 (tpp) cc_final: 0.9088 (mtp) REVERT: B 133 TRP cc_start: 0.7414 (OUTLIER) cc_final: 0.7207 (m-10) REVERT: B 169 ASP cc_start: 0.8767 (p0) cc_final: 0.8521 (p0) REVERT: B 215 ARG cc_start: 0.8585 (tpp-160) cc_final: 0.8075 (tpt170) REVERT: C 20 ILE cc_start: 0.8594 (mp) cc_final: 0.8275 (mp) REVERT: C 46 ASP cc_start: 0.9003 (p0) cc_final: 0.8726 (p0) REVERT: C 66 ASP cc_start: 0.9028 (t70) cc_final: 0.8657 (t0) REVERT: C 93 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8842 (mmm) REVERT: C 203 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9112 (mp) REVERT: C 215 ARG cc_start: 0.8627 (tpp-160) cc_final: 0.8197 (tpt170) REVERT: D 66 ASP cc_start: 0.9041 (t70) cc_final: 0.8746 (t0) REVERT: D 133 TRP cc_start: 0.7397 (OUTLIER) cc_final: 0.7162 (m-10) REVERT: D 211 TYR cc_start: 0.8588 (t80) cc_final: 0.8333 (t80) REVERT: D 215 ARG cc_start: 0.8655 (tpp-160) cc_final: 0.8149 (tpt170) REVERT: E 66 ASP cc_start: 0.9011 (t70) cc_final: 0.8558 (t0) REVERT: E 93 MET cc_start: 0.9385 (tpp) cc_final: 0.9111 (mtp) REVERT: E 133 TRP cc_start: 0.7397 (OUTLIER) cc_final: 0.7185 (m-10) REVERT: E 169 ASP cc_start: 0.8798 (p0) cc_final: 0.8565 (p0) REVERT: E 215 ARG cc_start: 0.8551 (tpp-160) cc_final: 0.8076 (tpt170) REVERT: F 46 ASP cc_start: 0.8976 (p0) cc_final: 0.8710 (p0) REVERT: F 66 ASP cc_start: 0.9023 (t70) cc_final: 0.8654 (t0) REVERT: F 93 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.8949 (mmm) REVERT: F 133 TRP cc_start: 0.7462 (OUTLIER) cc_final: 0.7259 (m-10) REVERT: F 203 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9100 (mp) REVERT: F 215 ARG cc_start: 0.8612 (tpp-160) cc_final: 0.8189 (tpt170) REVERT: G 66 ASP cc_start: 0.9045 (t70) cc_final: 0.8746 (t0) REVERT: G 133 TRP cc_start: 0.7403 (OUTLIER) cc_final: 0.7171 (m-10) REVERT: G 211 TYR cc_start: 0.8568 (t80) cc_final: 0.8304 (t80) REVERT: G 215 ARG cc_start: 0.8662 (tpp-160) cc_final: 0.8145 (tpt170) REVERT: H 66 ASP cc_start: 0.9017 (t70) cc_final: 0.8560 (t0) REVERT: H 93 MET cc_start: 0.9413 (tpp) cc_final: 0.9072 (mtp) REVERT: H 133 TRP cc_start: 0.7413 (OUTLIER) cc_final: 0.7207 (m-10) REVERT: H 169 ASP cc_start: 0.8831 (p0) cc_final: 0.8594 (p0) REVERT: H 215 ARG cc_start: 0.8612 (tpp-160) cc_final: 0.8093 (tpt170) REVERT: I 20 ILE cc_start: 0.8616 (mp) cc_final: 0.8306 (mp) REVERT: I 46 ASP cc_start: 0.8986 (p0) cc_final: 0.8723 (p0) REVERT: I 66 ASP cc_start: 0.9033 (t70) cc_final: 0.8664 (t0) REVERT: I 93 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.8854 (mmm) REVERT: I 133 TRP cc_start: 0.7445 (OUTLIER) cc_final: 0.7235 (m-10) REVERT: I 215 ARG cc_start: 0.8622 (tpp-160) cc_final: 0.8163 (tpt170) REVERT: J 66 ASP cc_start: 0.9079 (t70) cc_final: 0.8782 (t0) REVERT: J 133 TRP cc_start: 0.7420 (OUTLIER) cc_final: 0.7212 (m-10) REVERT: J 211 TYR cc_start: 0.8586 (t80) cc_final: 0.8326 (t80) REVERT: J 215 ARG cc_start: 0.8671 (tpp-160) cc_final: 0.8131 (tpt170) REVERT: K 66 ASP cc_start: 0.9008 (t70) cc_final: 0.8547 (t0) REVERT: K 93 MET cc_start: 0.9399 (tpp) cc_final: 0.9054 (mtp) REVERT: K 133 TRP cc_start: 0.7434 (OUTLIER) cc_final: 0.7228 (m-10) REVERT: K 169 ASP cc_start: 0.8834 (p0) cc_final: 0.8602 (p0) REVERT: K 215 ARG cc_start: 0.8583 (tpp-160) cc_final: 0.8077 (tpt170) REVERT: L 20 ILE cc_start: 0.8607 (mp) cc_final: 0.8294 (mp) REVERT: L 46 ASP cc_start: 0.8979 (p0) cc_final: 0.8709 (p0) REVERT: L 66 ASP cc_start: 0.9051 (t70) cc_final: 0.8683 (t0) REVERT: L 93 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.9063 (mmt) REVERT: L 94 HIS cc_start: 0.8730 (t70) cc_final: 0.8490 (t70) REVERT: L 215 ARG cc_start: 0.8608 (tpp-160) cc_final: 0.8165 (tpt170) outliers start: 82 outliers final: 19 residues processed: 364 average time/residue: 1.2459 time to fit residues: 505.9572 Evaluate side-chains 323 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 287 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET 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 B residue 214 ILE Chi-restraints excluded: chain C residue 71 ILE 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 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 E residue 214 ILE 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 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 H residue 214 ILE 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 K residue 214 ILE 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: 6.9990 chunk 145 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 94 HIS 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 80 GLN 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 94 HIS I 175 ASN J 54 ASN J 175 ASN K 54 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.095094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.074124 restraints weight = 31356.256| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.20 r_work: 0.2940 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2569 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 : 0.473 5.189 23388 Z= 0.251 Chirality : 0.042 0.251 2796 Planarity : 0.003 0.018 2784 Dihedral : 3.152 10.272 2232 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.52 % Allowed : 18.44 % Favored : 77.04 % 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: 3.04 (0.17), residues: 2028 helix: 3.21 (0.12), residues: 1404 sheet: 1.08 (0.46), residues: 132 loop : -1.56 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 133 HIS 0.004 0.001 HIS I 97 PHE 0.009 0.001 PHE H 180 TYR 0.008 0.001 TYR B 65 ARG 0.006 0.000 ARG D 22 Details of bonding type rmsd hydrogen bonds : bond 0.02876 ( 1224) hydrogen bonds : angle 3.13309 ( 3636) SS BOND : bond 0.00135 ( 36) SS BOND : angle 0.65550 ( 72) covalent geometry : bond 0.00273 (17052) covalent geometry : angle 0.47192 (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: 84 poor density : 315 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8556 (mp) cc_final: 0.8293 (mp) REVERT: A 66 ASP cc_start: 0.9072 (t70) cc_final: 0.8764 (t0) REVERT: A 93 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8831 (mmt) REVERT: A 133 TRP cc_start: 0.7393 (OUTLIER) cc_final: 0.7190 (m-10) REVERT: A 215 ARG cc_start: 0.8677 (tpp-160) cc_final: 0.8109 (tpt170) REVERT: B 46 ASP cc_start: 0.8840 (p0) cc_final: 0.8637 (p0) REVERT: B 66 ASP cc_start: 0.9019 (t70) cc_final: 0.8559 (t0) REVERT: B 93 MET cc_start: 0.9379 (tpp) cc_final: 0.9125 (mtp) REVERT: B 133 TRP cc_start: 0.7379 (OUTLIER) cc_final: 0.7172 (m-10) REVERT: B 169 ASP cc_start: 0.8767 (p0) cc_final: 0.8532 (p0) REVERT: B 215 ARG cc_start: 0.8597 (tpp-160) cc_final: 0.8074 (tpt170) REVERT: C 20 ILE cc_start: 0.8570 (mp) cc_final: 0.8272 (mp) REVERT: C 66 ASP cc_start: 0.9050 (t70) cc_final: 0.8688 (t0) REVERT: C 93 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.8888 (mmm) REVERT: C 133 TRP cc_start: 0.7504 (m-10) cc_final: 0.7262 (m-10) REVERT: C 203 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.9106 (mp) REVERT: C 215 ARG cc_start: 0.8610 (tpp-160) cc_final: 0.8186 (tpt170) REVERT: D 46 ASP cc_start: 0.8779 (p0) cc_final: 0.8573 (p0) REVERT: D 66 ASP cc_start: 0.9034 (t70) cc_final: 0.8729 (t0) REVERT: D 133 TRP cc_start: 0.7348 (OUTLIER) cc_final: 0.7146 (m-10) REVERT: D 211 TYR cc_start: 0.8585 (t80) cc_final: 0.8317 (t80) REVERT: D 215 ARG cc_start: 0.8654 (tpp-160) cc_final: 0.8116 (tpt170) REVERT: E 46 ASP cc_start: 0.8839 (p0) cc_final: 0.8636 (p0) REVERT: E 66 ASP cc_start: 0.9016 (t70) cc_final: 0.8557 (t0) REVERT: E 93 MET cc_start: 0.9401 (tpp) cc_final: 0.9099 (mtp) REVERT: E 133 TRP cc_start: 0.7355 (OUTLIER) cc_final: 0.7145 (m-10) REVERT: E 169 ASP cc_start: 0.8781 (p0) cc_final: 0.8557 (p0) REVERT: E 215 ARG cc_start: 0.8560 (tpp-160) cc_final: 0.8072 (tpt170) REVERT: F 20 ILE cc_start: 0.8601 (mp) cc_final: 0.8314 (mp) REVERT: F 66 ASP cc_start: 0.9060 (t70) cc_final: 0.8699 (t0) REVERT: F 93 MET cc_start: 0.9418 (OUTLIER) cc_final: 0.8820 (mmm) REVERT: F 203 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9102 (mp) REVERT: F 215 ARG cc_start: 0.8593 (tpp-160) cc_final: 0.8185 (tpt170) REVERT: G 66 ASP cc_start: 0.9064 (t70) cc_final: 0.8758 (t0) REVERT: G 133 TRP cc_start: 0.7345 (OUTLIER) cc_final: 0.7145 (m-10) REVERT: G 211 TYR cc_start: 0.8576 (t80) cc_final: 0.8305 (t80) REVERT: G 215 ARG cc_start: 0.8639 (tpp-160) cc_final: 0.8113 (tpt170) REVERT: H 66 ASP cc_start: 0.9035 (t70) cc_final: 0.8640 (t0) REVERT: H 93 MET cc_start: 0.9432 (tpp) cc_final: 0.9077 (mtp) REVERT: H 133 TRP cc_start: 0.7370 (OUTLIER) cc_final: 0.7164 (m-10) REVERT: H 169 ASP cc_start: 0.8813 (p0) cc_final: 0.8574 (p0) REVERT: H 215 ARG cc_start: 0.8616 (tpp-160) cc_final: 0.8084 (tpt170) REVERT: I 20 ILE cc_start: 0.8606 (mp) cc_final: 0.8309 (mp) REVERT: I 66 ASP cc_start: 0.9045 (t70) cc_final: 0.8674 (t0) REVERT: I 93 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8901 (mmm) REVERT: I 215 ARG cc_start: 0.8617 (tpp-160) cc_final: 0.8181 (tpt170) REVERT: J 46 ASP cc_start: 0.8799 (p0) cc_final: 0.8592 (p0) REVERT: J 66 ASP cc_start: 0.9087 (t70) cc_final: 0.8789 (t0) REVERT: J 133 TRP cc_start: 0.7374 (OUTLIER) cc_final: 0.7164 (m-10) REVERT: J 211 TYR cc_start: 0.8592 (t80) cc_final: 0.8320 (t80) REVERT: J 215 ARG cc_start: 0.8666 (tpp-160) cc_final: 0.8124 (tpt170) REVERT: K 46 ASP cc_start: 0.8879 (p0) cc_final: 0.8678 (p0) REVERT: K 66 ASP cc_start: 0.9034 (t70) cc_final: 0.8580 (t0) REVERT: K 93 MET cc_start: 0.9397 (tpp) cc_final: 0.9027 (mtp) REVERT: K 133 TRP cc_start: 0.7396 (OUTLIER) cc_final: 0.7193 (m-10) REVERT: K 169 ASP cc_start: 0.8800 (p0) cc_final: 0.8557 (p0) REVERT: K 215 ARG cc_start: 0.8595 (tpp-160) cc_final: 0.8084 (tpt170) REVERT: L 20 ILE cc_start: 0.8599 (mp) cc_final: 0.8301 (mp) REVERT: L 66 ASP cc_start: 0.9064 (t70) cc_final: 0.8704 (t0) REVERT: L 93 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.9097 (mmt) REVERT: L 94 HIS cc_start: 0.8685 (t70) cc_final: 0.8450 (t70) REVERT: L 215 ARG cc_start: 0.8598 (tpp-160) cc_final: 0.8182 (tpt170) outliers start: 84 outliers final: 15 residues processed: 360 average time/residue: 1.1971 time to fit residues: 480.9367 Evaluate side-chains 314 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 284 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET 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 71 ILE 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 71 ILE Chi-restraints excluded: chain F residue 93 MET 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 I residue 93 MET 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 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 Chi-restraints excluded: chain L residue 214 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 114 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 154 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 22 optimal weight: 0.0470 chunk 20 optimal weight: 0.0870 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 ** 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 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 G 205 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.094988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.074808 restraints weight = 31523.764| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.14 r_work: 0.2898 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17088 Z= 0.105 Angle : 0.463 5.152 23388 Z= 0.246 Chirality : 0.041 0.246 2796 Planarity : 0.003 0.022 2784 Dihedral : 3.110 10.534 2232 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.68 % Allowed : 19.46 % Favored : 75.86 % 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: 3.13 (0.17), residues: 2028 helix: 3.27 (0.12), residues: 1404 sheet: 1.11 (0.47), residues: 132 loop : -1.52 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 133 HIS 0.010 0.001 HIS I 94 PHE 0.009 0.001 PHE H 180 TYR 0.007 0.001 TYR D 135 ARG 0.005 0.000 ARG D 22 Details of bonding type rmsd hydrogen bonds : bond 0.02782 ( 1224) hydrogen bonds : angle 3.07929 ( 3636) SS BOND : bond 0.00127 ( 36) SS BOND : angle 0.56276 ( 72) covalent geometry : bond 0.00233 (17052) covalent geometry : angle 0.46279 (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 416 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 329 time to evaluate : 2.147 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: 0.8488 (mp) cc_final: 0.8258 (mp) REVERT: A 66 ASP cc_start: 0.9027 (t70) cc_final: 0.8709 (t0) REVERT: A 93 MET cc_start: 0.9024 (mmt) cc_final: 0.8817 (mmt) REVERT: A 215 ARG cc_start: 0.8613 (tpp-160) cc_final: 0.8088 (tpt170) REVERT: B 46 ASP cc_start: 0.8838 (p0) cc_final: 0.8594 (p0) REVERT: B 66 ASP cc_start: 0.8948 (t70) cc_final: 0.8478 (t0) REVERT: B 93 MET cc_start: 0.9416 (tpp) cc_final: 0.9149 (mtp) REVERT: B 169 ASP cc_start: 0.8683 (p0) cc_final: 0.8481 (p0) REVERT: B 215 ARG cc_start: 0.8594 (tpp-160) cc_final: 0.8078 (tpt170) REVERT: C 20 ILE cc_start: 0.8561 (mp) cc_final: 0.8283 (mp) REVERT: C 66 ASP cc_start: 0.9019 (t70) cc_final: 0.8646 (t0) REVERT: C 93 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.8865 (mmm) REVERT: C 133 TRP cc_start: 0.7373 (m-10) cc_final: 0.7067 (m-10) REVERT: C 203 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9070 (mp) REVERT: C 215 ARG cc_start: 0.8614 (tpp-160) cc_final: 0.8181 (tpt170) REVERT: D 46 ASP cc_start: 0.8730 (p0) cc_final: 0.8487 (p0) REVERT: D 66 ASP cc_start: 0.9001 (t70) cc_final: 0.8685 (t0) REVERT: D 133 TRP cc_start: 0.7340 (OUTLIER) cc_final: 0.7131 (m-10) REVERT: D 211 TYR cc_start: 0.8575 (t80) cc_final: 0.8279 (t80) REVERT: D 215 ARG cc_start: 0.8628 (tpp-160) cc_final: 0.8125 (tpt170) REVERT: E 46 ASP cc_start: 0.8850 (p0) cc_final: 0.8606 (p0) REVERT: E 66 ASP cc_start: 0.8970 (t70) cc_final: 0.8494 (t0) REVERT: E 93 MET cc_start: 0.9412 (tpp) cc_final: 0.9146 (mtp) REVERT: E 169 ASP cc_start: 0.8680 (p0) cc_final: 0.8472 (p0) REVERT: E 215 ARG cc_start: 0.8613 (tpp-160) cc_final: 0.8069 (tpt170) REVERT: F 20 ILE cc_start: 0.8573 (mp) cc_final: 0.8313 (mp) REVERT: F 47 GLU cc_start: 0.8784 (pt0) cc_final: 0.8578 (pt0) REVERT: F 66 ASP cc_start: 0.9026 (t70) cc_final: 0.8658 (t0) REVERT: F 93 MET cc_start: 0.9442 (OUTLIER) cc_final: 0.8809 (mmm) REVERT: F 133 TRP cc_start: 0.7357 (m-10) cc_final: 0.7081 (m-10) REVERT: F 203 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9066 (mp) REVERT: F 215 ARG cc_start: 0.8662 (tpp-160) cc_final: 0.8189 (tpt170) REVERT: G 66 ASP cc_start: 0.9010 (t70) cc_final: 0.8695 (t0) REVERT: G 133 TRP cc_start: 0.7322 (OUTLIER) cc_final: 0.7112 (m-10) REVERT: G 211 TYR cc_start: 0.8575 (t80) cc_final: 0.8261 (t80) REVERT: G 215 ARG cc_start: 0.8631 (tpp-160) cc_final: 0.8122 (tpt170) REVERT: H 66 ASP cc_start: 0.8987 (t70) cc_final: 0.8518 (t0) REVERT: H 93 MET cc_start: 0.9437 (tpp) cc_final: 0.9084 (mtp) REVERT: H 133 TRP cc_start: 0.7374 (OUTLIER) cc_final: 0.7168 (m-10) REVERT: H 169 ASP cc_start: 0.8730 (p0) cc_final: 0.8527 (p0) REVERT: H 215 ARG cc_start: 0.8607 (tpp-160) cc_final: 0.8083 (tpt170) REVERT: I 20 ILE cc_start: 0.8591 (mp) cc_final: 0.8330 (mp) REVERT: I 66 ASP cc_start: 0.9024 (t70) cc_final: 0.8652 (t0) REVERT: I 93 MET cc_start: 0.9406 (OUTLIER) cc_final: 0.8877 (mmm) REVERT: I 133 TRP cc_start: 0.7344 (m-10) cc_final: 0.7076 (m-10) REVERT: I 215 ARG cc_start: 0.8645 (tpp-160) cc_final: 0.8176 (tpt170) REVERT: J 46 ASP cc_start: 0.8724 (p0) cc_final: 0.8482 (p0) REVERT: J 66 ASP cc_start: 0.9037 (t70) cc_final: 0.8725 (t0) REVERT: J 133 TRP cc_start: 0.7377 (OUTLIER) cc_final: 0.7135 (m-10) REVERT: J 211 TYR cc_start: 0.8583 (t80) cc_final: 0.8320 (t80) REVERT: J 215 ARG cc_start: 0.8663 (tpp-160) cc_final: 0.8130 (tpt170) REVERT: K 46 ASP cc_start: 0.8825 (p0) cc_final: 0.8588 (p0) REVERT: K 66 ASP cc_start: 0.8970 (t70) cc_final: 0.8496 (t0) REVERT: K 93 MET cc_start: 0.9426 (tpp) cc_final: 0.9060 (mtp) REVERT: K 133 TRP cc_start: 0.7355 (OUTLIER) cc_final: 0.7149 (m-10) REVERT: K 169 ASP cc_start: 0.8719 (p0) cc_final: 0.8514 (p0) REVERT: K 215 ARG cc_start: 0.8604 (tpp-160) cc_final: 0.8082 (tpt170) REVERT: L 20 ILE cc_start: 0.8589 (mp) cc_final: 0.8323 (mp) REVERT: L 66 ASP cc_start: 0.9028 (t70) cc_final: 0.8660 (t0) REVERT: L 93 MET cc_start: 0.9384 (OUTLIER) cc_final: 0.9108 (mmt) REVERT: L 94 HIS cc_start: 0.8726 (t70) cc_final: 0.8475 (t70) REVERT: L 215 ARG cc_start: 0.8624 (tpp-160) cc_final: 0.8174 (tpt170) outliers start: 87 outliers final: 17 residues processed: 386 average time/residue: 1.1526 time to fit residues: 499.6325 Evaluate side-chains 320 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 71 ILE 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 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain F residue 93 MET 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 H residue 133 TRP 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 133 TRP 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 133 TRP Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 140 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 193 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 13 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 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 J 205 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.073117 restraints weight = 31455.983| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.14 r_work: 0.2862 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17088 Z= 0.153 Angle : 0.504 5.284 23388 Z= 0.268 Chirality : 0.042 0.236 2796 Planarity : 0.003 0.021 2784 Dihedral : 3.140 10.654 2232 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.41 % Allowed : 20.91 % Favored : 74.68 % 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: 3.13 (0.17), residues: 2028 helix: 3.24 (0.12), residues: 1404 sheet: 1.30 (0.47), residues: 132 loop : -1.46 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 44 HIS 0.007 0.001 HIS C 94 PHE 0.011 0.001 PHE L 68 TYR 0.010 0.001 TYR E 65 ARG 0.004 0.000 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.02801 ( 1224) hydrogen bonds : angle 3.08181 ( 3636) SS BOND : bond 0.00174 ( 36) SS BOND : angle 0.76904 ( 72) covalent geometry : bond 0.00358 (17052) covalent geometry : angle 0.50269 (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 398 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 316 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8571 (mp) cc_final: 0.8338 (mp) REVERT: A 54 ASN cc_start: 0.9117 (OUTLIER) cc_final: 0.8887 (t0) REVERT: A 66 ASP cc_start: 0.9102 (t70) cc_final: 0.8778 (t0) REVERT: A 93 MET cc_start: 0.9042 (mmt) cc_final: 0.8821 (mmt) REVERT: A 215 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8102 (tpt170) REVERT: B 46 ASP cc_start: 0.8912 (p0) cc_final: 0.8646 (p0) REVERT: B 66 ASP cc_start: 0.9039 (t70) cc_final: 0.8560 (t0) REVERT: B 80 GLN cc_start: 0.9413 (tt0) cc_final: 0.9210 (tt0) REVERT: B 93 MET cc_start: 0.9431 (tpp) cc_final: 0.9112 (mtp) REVERT: B 133 TRP cc_start: 0.7383 (m-10) cc_final: 0.7175 (m-10) REVERT: B 169 ASP cc_start: 0.8710 (p0) cc_final: 0.8474 (p0) REVERT: B 215 ARG cc_start: 0.8576 (tpp-160) cc_final: 0.8077 (tpt170) REVERT: C 20 ILE cc_start: 0.8578 (mp) cc_final: 0.8328 (mp) REVERT: C 46 ASP cc_start: 0.8854 (p0) cc_final: 0.8645 (p0) REVERT: C 66 ASP cc_start: 0.9103 (t70) cc_final: 0.8713 (t0) REVERT: C 93 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.9108 (mmm) REVERT: C 133 TRP cc_start: 0.7336 (m-10) cc_final: 0.7044 (m-10) REVERT: C 203 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9072 (mp) REVERT: C 215 ARG cc_start: 0.8625 (tpp-160) cc_final: 0.8185 (tpt170) REVERT: D 46 ASP cc_start: 0.8790 (p0) cc_final: 0.8550 (p0) REVERT: D 66 ASP cc_start: 0.9091 (t70) cc_final: 0.8766 (t0) REVERT: D 133 TRP cc_start: 0.7319 (OUTLIER) cc_final: 0.7116 (m-10) REVERT: D 211 TYR cc_start: 0.8565 (t80) cc_final: 0.8304 (t80) REVERT: D 215 ARG cc_start: 0.8649 (tpp-160) cc_final: 0.8122 (tpt170) REVERT: E 46 ASP cc_start: 0.8912 (p0) cc_final: 0.8644 (p0) REVERT: E 66 ASP cc_start: 0.9052 (t70) cc_final: 0.8572 (t0) REVERT: E 93 MET cc_start: 0.9426 (tpp) cc_final: 0.9107 (mtp) REVERT: E 133 TRP cc_start: 0.7406 (m-10) cc_final: 0.7194 (m-10) REVERT: E 169 ASP cc_start: 0.8751 (p0) cc_final: 0.8518 (p0) REVERT: E 215 ARG cc_start: 0.8604 (tpp-160) cc_final: 0.8069 (tpt170) REVERT: F 20 ILE cc_start: 0.8614 (mp) cc_final: 0.8357 (mp) REVERT: F 46 ASP cc_start: 0.8867 (p0) cc_final: 0.8657 (p0) REVERT: F 66 ASP cc_start: 0.9106 (t70) cc_final: 0.8722 (t0) REVERT: F 93 MET cc_start: 0.9445 (OUTLIER) cc_final: 0.9139 (mmt) REVERT: F 133 TRP cc_start: 0.7334 (m-10) cc_final: 0.7045 (m-10) REVERT: F 203 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9067 (mp) REVERT: F 215 ARG cc_start: 0.8636 (tpp-160) cc_final: 0.8184 (tpt170) REVERT: G 66 ASP cc_start: 0.9105 (t70) cc_final: 0.8779 (t0) REVERT: G 211 TYR cc_start: 0.8553 (t80) cc_final: 0.8272 (t80) REVERT: G 215 ARG cc_start: 0.8648 (tpp-160) cc_final: 0.8135 (tpt170) REVERT: H 66 ASP cc_start: 0.9064 (t70) cc_final: 0.8579 (t0) REVERT: H 80 GLN cc_start: 0.9419 (tt0) cc_final: 0.9190 (tt0) REVERT: H 93 MET cc_start: 0.9447 (tpp) cc_final: 0.9075 (mtp) REVERT: H 169 ASP cc_start: 0.8752 (p0) cc_final: 0.8524 (p0) REVERT: H 215 ARG cc_start: 0.8594 (tpp-160) cc_final: 0.8080 (tpt170) REVERT: I 20 ILE cc_start: 0.8622 (mp) cc_final: 0.8371 (mp) REVERT: I 66 ASP cc_start: 0.9112 (t70) cc_final: 0.8717 (t0) REVERT: I 93 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.9115 (mmm) REVERT: I 133 TRP cc_start: 0.7313 (m-10) cc_final: 0.7025 (m-10) REVERT: I 215 ARG cc_start: 0.8638 (tpp-160) cc_final: 0.8178 (tpt170) REVERT: J 46 ASP cc_start: 0.8815 (p0) cc_final: 0.8580 (p0) REVERT: J 66 ASP cc_start: 0.9108 (t70) cc_final: 0.8781 (t0) REVERT: J 133 TRP cc_start: 0.7362 (OUTLIER) cc_final: 0.7124 (m-10) REVERT: J 211 TYR cc_start: 0.8570 (t80) cc_final: 0.8302 (t80) REVERT: J 215 ARG cc_start: 0.8660 (tpp-160) cc_final: 0.8143 (tpt170) REVERT: K 46 ASP cc_start: 0.8903 (p0) cc_final: 0.8668 (p0) REVERT: K 66 ASP cc_start: 0.9067 (t70) cc_final: 0.8583 (t0) REVERT: K 80 GLN cc_start: 0.9369 (tt0) cc_final: 0.9153 (tt0) REVERT: K 93 MET cc_start: 0.9433 (tpp) cc_final: 0.9043 (mtp) REVERT: K 169 ASP cc_start: 0.8743 (p0) cc_final: 0.8512 (p0) REVERT: K 215 ARG cc_start: 0.8592 (tpp-160) cc_final: 0.8075 (tpt170) REVERT: L 20 ILE cc_start: 0.8613 (mp) cc_final: 0.8358 (mp) REVERT: L 66 ASP cc_start: 0.9115 (t70) cc_final: 0.8720 (t0) REVERT: L 93 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.9132 (mmt) REVERT: L 215 ARG cc_start: 0.8615 (tpp-160) cc_final: 0.8171 (tpt170) outliers start: 82 outliers final: 16 residues processed: 370 average time/residue: 1.1930 time to fit residues: 495.9883 Evaluate side-chains 317 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 292 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain C residue 80 GLN 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 D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR 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 134 THR Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 134 THR 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 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: 0.7980 chunk 22 optimal weight: 0.8980 chunk 192 optimal weight: 0.5980 chunk 176 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 181 optimal weight: 0.1980 chunk 172 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 D 205 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.095896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.074966 restraints weight = 31058.404| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.19 r_work: 0.2952 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17088 Z= 0.115 Angle : 0.491 5.149 23388 Z= 0.262 Chirality : 0.041 0.219 2796 Planarity : 0.003 0.025 2784 Dihedral : 3.157 11.104 2232 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.76 % Allowed : 21.18 % 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: 3.10 (0.17), residues: 2028 helix: 3.22 (0.12), residues: 1404 sheet: 1.28 (0.48), residues: 132 loop : -1.48 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 133 HIS 0.010 0.001 HIS L 94 PHE 0.008 0.001 PHE L 180 TYR 0.008 0.001 TYR H 65 ARG 0.004 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.02738 ( 1224) hydrogen bonds : angle 3.09609 ( 3636) SS BOND : bond 0.00141 ( 36) SS BOND : angle 0.59433 ( 72) covalent geometry : bond 0.00262 (17052) covalent geometry : angle 0.49094 (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 373 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 303 time to evaluate : 2.405 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: 0.8534 (mp) cc_final: 0.8326 (mp) REVERT: A 66 ASP cc_start: 0.9086 (t70) cc_final: 0.8755 (t0) REVERT: A 93 MET cc_start: 0.9061 (mmt) cc_final: 0.8818 (mmt) REVERT: A 215 ARG cc_start: 0.8632 (tpp-160) cc_final: 0.8115 (tpt170) REVERT: B 46 ASP cc_start: 0.8929 (p0) cc_final: 0.8666 (p0) REVERT: B 66 ASP cc_start: 0.9049 (t70) cc_final: 0.8589 (t0) REVERT: B 93 MET cc_start: 0.9424 (tpp) cc_final: 0.9117 (mtp) REVERT: B 133 TRP cc_start: 0.7362 (m-10) cc_final: 0.7118 (m-10) REVERT: B 215 ARG cc_start: 0.8644 (tpp-160) cc_final: 0.8100 (tpt170) REVERT: C 20 ILE cc_start: 0.8511 (mp) cc_final: 0.8268 (mp) REVERT: C 66 ASP cc_start: 0.9100 (t70) cc_final: 0.8724 (t0) REVERT: C 93 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.9076 (mmm) REVERT: C 133 TRP cc_start: 0.7387 (m-10) cc_final: 0.7099 (m-10) REVERT: C 203 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9075 (mp) REVERT: C 215 ARG cc_start: 0.8607 (tpp-160) cc_final: 0.8196 (tpt170) REVERT: D 46 ASP cc_start: 0.8811 (p0) cc_final: 0.8590 (p0) REVERT: D 66 ASP cc_start: 0.9070 (t70) cc_final: 0.8739 (t0) REVERT: D 211 TYR cc_start: 0.8569 (t80) cc_final: 0.8303 (t80) REVERT: D 215 ARG cc_start: 0.8700 (tpp-160) cc_final: 0.8148 (tpt170) REVERT: E 46 ASP cc_start: 0.8935 (p0) cc_final: 0.8688 (p0) REVERT: E 66 ASP cc_start: 0.9069 (t70) cc_final: 0.8611 (t0) REVERT: E 93 MET cc_start: 0.9429 (tpp) cc_final: 0.9125 (mtp) REVERT: E 133 TRP cc_start: 0.7349 (m-10) cc_final: 0.7106 (m-10) REVERT: E 215 ARG cc_start: 0.8622 (tpp-160) cc_final: 0.8095 (tpt170) REVERT: F 20 ILE cc_start: 0.8544 (mp) cc_final: 0.8304 (mp) REVERT: F 46 ASP cc_start: 0.8822 (p0) cc_final: 0.8604 (p0) REVERT: F 66 ASP cc_start: 0.9101 (t70) cc_final: 0.8727 (t0) REVERT: F 93 MET cc_start: 0.9418 (OUTLIER) cc_final: 0.8771 (mmm) REVERT: F 133 TRP cc_start: 0.7362 (m-10) cc_final: 0.7075 (m-10) REVERT: F 203 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9063 (mp) REVERT: F 215 ARG cc_start: 0.8604 (tpp-160) cc_final: 0.8185 (tpt170) REVERT: G 66 ASP cc_start: 0.9079 (t70) cc_final: 0.8755 (t0) REVERT: G 211 TYR cc_start: 0.8571 (t80) cc_final: 0.8295 (t80) REVERT: G 215 ARG cc_start: 0.8680 (tpp-160) cc_final: 0.8145 (tpt170) REVERT: H 66 ASP cc_start: 0.9094 (t70) cc_final: 0.8624 (t0) REVERT: H 80 GLN cc_start: 0.9373 (tt0) cc_final: 0.9155 (tt0) REVERT: H 93 MET cc_start: 0.9446 (tpp) cc_final: 0.9059 (mtp) REVERT: H 215 ARG cc_start: 0.8668 (tpp-160) cc_final: 0.8109 (tpt170) REVERT: I 20 ILE cc_start: 0.8583 (mp) cc_final: 0.8355 (mp) REVERT: I 66 ASP cc_start: 0.9100 (t70) cc_final: 0.8716 (t0) REVERT: I 93 MET cc_start: 0.9384 (OUTLIER) cc_final: 0.9039 (mmm) REVERT: I 133 TRP cc_start: 0.7367 (m-10) cc_final: 0.7108 (m-10) REVERT: I 215 ARG cc_start: 0.8607 (tpp-160) cc_final: 0.8171 (tpt170) REVERT: J 46 ASP cc_start: 0.8832 (p0) cc_final: 0.8622 (p0) REVERT: J 66 ASP cc_start: 0.9092 (t70) cc_final: 0.8771 (t0) REVERT: J 211 TYR cc_start: 0.8572 (t80) cc_final: 0.8304 (t80) REVERT: J 215 ARG cc_start: 0.8681 (tpp-160) cc_final: 0.8145 (tpt170) REVERT: K 46 ASP cc_start: 0.8893 (p0) cc_final: 0.8673 (p0) REVERT: K 66 ASP cc_start: 0.9090 (t70) cc_final: 0.8615 (t0) REVERT: K 93 MET cc_start: 0.9428 (tpp) cc_final: 0.9020 (mtp) REVERT: K 133 TRP cc_start: 0.7343 (m-10) cc_final: 0.7140 (m-10) REVERT: K 215 ARG cc_start: 0.8657 (tpp-160) cc_final: 0.8099 (tpt170) REVERT: L 20 ILE cc_start: 0.8590 (mp) cc_final: 0.8361 (mp) REVERT: L 66 ASP cc_start: 0.9099 (t70) cc_final: 0.8713 (t0) REVERT: L 93 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.9150 (mmt) REVERT: L 133 TRP cc_start: 0.7407 (m-10) cc_final: 0.7087 (m-10) REVERT: L 215 ARG cc_start: 0.8585 (tpp-160) cc_final: 0.8173 (tpt170) outliers start: 70 outliers final: 23 residues processed: 347 average time/residue: 1.3951 time to fit residues: 546.3772 Evaluate side-chains 324 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 295 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 134 THR 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 134 THR 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 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 80 GLN Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 134 THR 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 80 GLN Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 134 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 110 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 181 optimal weight: 0.0570 chunk 56 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 80 GLN 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: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.096526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.075558 restraints weight = 31134.710| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.21 r_work: 0.2963 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17088 Z= 0.123 Angle : 0.515 6.644 23388 Z= 0.280 Chirality : 0.041 0.189 2796 Planarity : 0.003 0.020 2784 Dihedral : 3.146 11.281 2232 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.17 % Allowed : 21.88 % Favored : 74.95 % Cbeta Deviations : 0.20 % 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: 3.13 (0.17), residues: 2028 helix: 3.23 (0.12), residues: 1404 sheet: 1.32 (0.47), residues: 132 loop : -1.41 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 133 HIS 0.007 0.001 HIS C 94 PHE 0.008 0.001 PHE I 180 TYR 0.007 0.001 TYR I 65 ARG 0.004 0.001 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.02704 ( 1224) hydrogen bonds : angle 3.06213 ( 3636) SS BOND : bond 0.00123 ( 36) SS BOND : angle 0.55846 ( 72) covalent geometry : bond 0.00278 (17052) covalent geometry : angle 0.51473 (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 365 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 306 time to evaluate : 1.944 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: 0.9061 (t70) cc_final: 0.8737 (t0) REVERT: A 93 MET cc_start: 0.9052 (mmt) cc_final: 0.8812 (mmt) REVERT: A 215 ARG cc_start: 0.8640 (tpp-160) cc_final: 0.8125 (tpt170) REVERT: B 46 ASP cc_start: 0.8940 (p0) cc_final: 0.8678 (p0) REVERT: B 66 ASP cc_start: 0.9030 (t70) cc_final: 0.8574 (t0) REVERT: B 93 MET cc_start: 0.9409 (tpp) cc_final: 0.9098 (mtp) REVERT: B 133 TRP cc_start: 0.7310 (m-10) cc_final: 0.7064 (m-10) REVERT: B 215 ARG cc_start: 0.8642 (tpp-160) cc_final: 0.8111 (tpt170) REVERT: C 20 ILE cc_start: 0.8466 (mp) cc_final: 0.8261 (mp) REVERT: C 93 MET cc_start: 0.9390 (tpp) cc_final: 0.9046 (mmm) REVERT: C 133 TRP cc_start: 0.7344 (m-10) cc_final: 0.6998 (m-10) REVERT: C 203 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9091 (mp) REVERT: C 215 ARG cc_start: 0.8596 (tpp-160) cc_final: 0.8187 (tpt170) REVERT: D 46 ASP cc_start: 0.8808 (p0) cc_final: 0.8562 (p0) REVERT: D 66 ASP cc_start: 0.9058 (t70) cc_final: 0.8735 (t0) REVERT: D 211 TYR cc_start: 0.8578 (t80) cc_final: 0.8306 (t80) REVERT: D 215 ARG cc_start: 0.8666 (tpp-160) cc_final: 0.8128 (tpt170) REVERT: E 46 ASP cc_start: 0.8947 (p0) cc_final: 0.8684 (p0) REVERT: E 66 ASP cc_start: 0.9047 (t70) cc_final: 0.8594 (t0) REVERT: E 93 MET cc_start: 0.9418 (tpp) cc_final: 0.9108 (mtp) REVERT: E 133 TRP cc_start: 0.7299 (m-10) cc_final: 0.7075 (m-10) REVERT: E 215 ARG cc_start: 0.8610 (tpp-160) cc_final: 0.8100 (tpt170) REVERT: F 20 ILE cc_start: 0.8538 (mp) cc_final: 0.8301 (mp) REVERT: F 66 ASP cc_start: 0.9076 (t70) cc_final: 0.8716 (t0) REVERT: F 133 TRP cc_start: 0.7306 (m-10) cc_final: 0.7039 (m-10) REVERT: F 203 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9080 (mp) REVERT: F 211 TYR cc_start: 0.8615 (t80) cc_final: 0.8177 (t80) REVERT: F 215 ARG cc_start: 0.8597 (tpp-160) cc_final: 0.8310 (tpt170) REVERT: G 66 ASP cc_start: 0.9069 (t70) cc_final: 0.8750 (t0) REVERT: G 211 TYR cc_start: 0.8569 (t80) cc_final: 0.8281 (t80) REVERT: G 215 ARG cc_start: 0.8652 (tpp-160) cc_final: 0.8129 (tpt170) REVERT: H 66 ASP cc_start: 0.9077 (t70) cc_final: 0.8617 (t0) REVERT: H 93 MET cc_start: 0.9451 (tpp) cc_final: 0.9051 (mtp) REVERT: H 215 ARG cc_start: 0.8647 (tpp-160) cc_final: 0.8103 (tpt170) REVERT: I 20 ILE cc_start: 0.8554 (mp) cc_final: 0.8329 (mp) REVERT: I 133 TRP cc_start: 0.7334 (m-10) cc_final: 0.7070 (m-10) REVERT: I 215 ARG cc_start: 0.8597 (tpp-160) cc_final: 0.8169 (tpt170) REVERT: J 20 ILE cc_start: 0.8621 (mp) cc_final: 0.8376 (mm) REVERT: J 46 ASP cc_start: 0.8828 (p0) cc_final: 0.8588 (p0) REVERT: J 66 ASP cc_start: 0.9071 (t70) cc_final: 0.8753 (t0) REVERT: J 211 TYR cc_start: 0.8591 (t80) cc_final: 0.8310 (t80) REVERT: J 215 ARG cc_start: 0.8639 (tpp-160) cc_final: 0.8125 (tpt170) REVERT: K 46 ASP cc_start: 0.8844 (p0) cc_final: 0.8584 (p0) REVERT: K 66 ASP cc_start: 0.9068 (t70) cc_final: 0.8609 (t0) REVERT: K 93 MET cc_start: 0.9426 (tpp) cc_final: 0.9007 (mtp) REVERT: K 133 TRP cc_start: 0.7283 (m-10) cc_final: 0.7076 (m-10) REVERT: K 215 ARG cc_start: 0.8643 (tpp-160) cc_final: 0.8107 (tpt170) REVERT: L 20 ILE cc_start: 0.8563 (mp) cc_final: 0.8333 (mp) REVERT: L 93 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.9117 (mmt) REVERT: L 133 TRP cc_start: 0.7376 (m-10) cc_final: 0.7015 (m-10) REVERT: L 215 ARG cc_start: 0.8576 (tpp-160) cc_final: 0.8169 (tpt170) outliers start: 59 outliers final: 20 residues processed: 346 average time/residue: 1.3173 time to fit residues: 510.3848 Evaluate side-chains 315 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 292 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 60 CYS 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 150 MET 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 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 K residue 150 MET 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 36 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 195 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 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 175 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.096343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.075372 restraints weight = 31168.716| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.21 r_work: 0.2958 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17088 Z= 0.130 Angle : 0.516 6.902 23388 Z= 0.278 Chirality : 0.041 0.163 2796 Planarity : 0.003 0.021 2784 Dihedral : 3.143 11.166 2232 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.06 % Allowed : 22.15 % 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: 3.15 (0.17), residues: 2028 helix: 3.22 (0.12), residues: 1404 sheet: 1.41 (0.48), residues: 132 loop : -1.34 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 44 HIS 0.007 0.001 HIS I 94 PHE 0.008 0.001 PHE I 180 TYR 0.008 0.001 TYR I 65 ARG 0.005 0.001 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.02694 ( 1224) hydrogen bonds : angle 3.05262 ( 3636) SS BOND : bond 0.00132 ( 36) SS BOND : angle 0.60099 ( 72) covalent geometry : bond 0.00300 (17052) covalent geometry : angle 0.51598 (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 366 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 309 time to evaluate : 1.833 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: 0.9056 (t70) cc_final: 0.8742 (t0) REVERT: A 93 MET cc_start: 0.9069 (mmt) cc_final: 0.8838 (mmt) REVERT: A 215 ARG cc_start: 0.8582 (tpp-160) cc_final: 0.8100 (tpt170) REVERT: B 46 ASP cc_start: 0.8926 (p0) cc_final: 0.8679 (p0) REVERT: B 66 ASP cc_start: 0.9047 (t70) cc_final: 0.8603 (t0) REVERT: B 93 MET cc_start: 0.9413 (tpp) cc_final: 0.9097 (mtp) REVERT: B 215 ARG cc_start: 0.8604 (tpp-160) cc_final: 0.8111 (tpt170) REVERT: C 93 MET cc_start: 0.9360 (tpp) cc_final: 0.9134 (mmm) REVERT: C 203 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9115 (mp) REVERT: C 211 TYR cc_start: 0.8661 (t80) cc_final: 0.8236 (t80) REVERT: C 215 ARG cc_start: 0.8558 (tpp-160) cc_final: 0.8301 (tpt170) REVERT: D 46 ASP cc_start: 0.8793 (p0) cc_final: 0.8567 (p0) REVERT: D 66 ASP cc_start: 0.9049 (t70) cc_final: 0.8728 (t0) REVERT: D 211 TYR cc_start: 0.8596 (t80) cc_final: 0.8328 (t80) REVERT: D 215 ARG cc_start: 0.8634 (tpp-160) cc_final: 0.8134 (tpt170) REVERT: E 46 ASP cc_start: 0.8921 (p0) cc_final: 0.8673 (p0) REVERT: E 66 ASP cc_start: 0.9055 (t70) cc_final: 0.8612 (t0) REVERT: E 93 MET cc_start: 0.9413 (tpp) cc_final: 0.9096 (mtp) REVERT: E 215 ARG cc_start: 0.8616 (tpp-160) cc_final: 0.8117 (tpt170) REVERT: F 20 ILE cc_start: 0.8516 (mp) cc_final: 0.8306 (mp) REVERT: F 203 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9113 (mp) REVERT: F 215 ARG cc_start: 0.8667 (tpp-160) cc_final: 0.8219 (tpt170) REVERT: G 66 ASP cc_start: 0.9051 (t70) cc_final: 0.8740 (t0) REVERT: G 211 TYR cc_start: 0.8587 (t80) cc_final: 0.8338 (t80) REVERT: G 215 ARG cc_start: 0.8624 (tpp-160) cc_final: 0.8120 (tpt170) REVERT: H 66 ASP cc_start: 0.9063 (t70) cc_final: 0.8605 (t0) REVERT: H 93 MET cc_start: 0.9447 (tpp) cc_final: 0.9036 (mtp) REVERT: H 215 ARG cc_start: 0.8626 (tpp-160) cc_final: 0.8106 (tpt170) REVERT: I 133 TRP cc_start: 0.7307 (m-10) cc_final: 0.7041 (m-10) REVERT: I 215 ARG cc_start: 0.8558 (tpp-160) cc_final: 0.8169 (tpt170) REVERT: J 20 ILE cc_start: 0.8652 (mp) cc_final: 0.8400 (mm) REVERT: J 46 ASP cc_start: 0.8815 (p0) cc_final: 0.8603 (p0) REVERT: J 66 ASP cc_start: 0.9070 (t70) cc_final: 0.8751 (t0) REVERT: J 211 TYR cc_start: 0.8604 (t80) cc_final: 0.8326 (t80) REVERT: J 215 ARG cc_start: 0.8613 (tpp-160) cc_final: 0.8121 (tpt170) REVERT: K 46 ASP cc_start: 0.8834 (p0) cc_final: 0.8615 (p0) REVERT: K 66 ASP cc_start: 0.9061 (t70) cc_final: 0.8607 (t0) REVERT: K 93 MET cc_start: 0.9421 (tpp) cc_final: 0.8987 (mtp) REVERT: K 215 ARG cc_start: 0.8611 (tpp-160) cc_final: 0.8104 (tpt170) REVERT: L 20 ILE cc_start: 0.8569 (mp) cc_final: 0.8357 (mp) REVERT: L 93 MET cc_start: 0.9398 (OUTLIER) cc_final: 0.9042 (mmm) REVERT: L 215 ARG cc_start: 0.8539 (tpp-160) cc_final: 0.8168 (tpt170) outliers start: 57 outliers final: 20 residues processed: 351 average time/residue: 1.1152 time to fit residues: 439.9509 Evaluate side-chains 323 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 300 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 203 ILE 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 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 H residue 150 MET Chi-restraints excluded: chain I residue 60 CYS 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 K residue 150 MET 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: 1.9990 chunk 65 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 172 optimal weight: 0.7980 chunk 183 optimal weight: 0.2980 chunk 105 optimal weight: 0.0670 chunk 192 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 97 HIS J 175 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 = 0.3505 r_free = 0.3505 target = 0.097145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.076210 restraints weight = 30974.461| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.20 r_work: 0.2978 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17088 Z= 0.121 Angle : 0.515 7.006 23388 Z= 0.278 Chirality : 0.040 0.155 2796 Planarity : 0.003 0.029 2784 Dihedral : 3.145 10.959 2232 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.96 % Allowed : 22.20 % Favored : 74.84 % 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: 3.20 (0.17), residues: 2028 helix: 3.24 (0.12), residues: 1404 sheet: 1.40 (0.47), residues: 132 loop : -1.27 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 132 HIS 0.009 0.001 HIS L 94 PHE 0.008 0.001 PHE I 180 TYR 0.007 0.001 TYR D 65 ARG 0.005 0.001 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.02660 ( 1224) hydrogen bonds : angle 3.03266 ( 3636) SS BOND : bond 0.00132 ( 36) SS BOND : angle 0.54941 ( 72) covalent geometry : bond 0.00273 (17052) covalent geometry : angle 0.51441 (23316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13490.99 seconds wall clock time: 235 minutes 35.40 seconds (14135.40 seconds total)