Starting phenix.real_space_refine on Sun Aug 24 02:29:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qjh_18447/08_2025/8qjh_18447_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qjh_18447/08_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_18447/08_2025/8qjh_18447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qjh_18447/08_2025/8qjh_18447.map" model { file = "/net/cci-nas-00/data/ceres_data/8qjh_18447/08_2025/8qjh_18447_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qjh_18447/08_2025/8qjh_18447_neut.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 1.60, per 1000 atoms: 0.10 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 B 53 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 179 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 179 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 179 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 179 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 179 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 173 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 173 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 173 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 173 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 173 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 168 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 168 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 168 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 168 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 168 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 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: 0.98 Conformation dependent library (CDL) restraints added in 555.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.46 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: 2.87 Time building geometry restraints manager: 1.33 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.290 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.260 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.001 0.000 ARG D 183 TYR 0.004 0.001 TYR G 151 PHE 0.005 0.001 PHE E 180 TRP 0.005 0.001 TRP K 77 HIS 0.001 0.000 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00175 (17052) covalent geometry : angle 0.40746 (23316) SS BOND : bond 0.00087 ( 36) SS BOND : angle 0.70696 ( 72) hydrogen bonds : bond 0.11055 ( 1224) hydrogen bonds : angle 4.64988 ( 3636) *********************** 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 : 0.694 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: 0.6133 time to fit residues: 339.8998 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 : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.0980 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.096660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.075777 restraints weight = 30648.625| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.17 r_work: 0.2973 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17088 Z= 0.122 Angle : 0.514 5.326 23388 Z= 0.272 Chirality : 0.043 0.203 2796 Planarity : 0.003 0.018 2784 Dihedral : 3.225 10.976 2232 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.82 % Allowed : 13.92 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.12 (0.18), residues: 2028 helix: 3.27 (0.12), residues: 1392 sheet: 1.00 (0.46), residues: 132 loop : -1.34 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 75 TYR 0.013 0.001 TYR F 211 PHE 0.009 0.001 PHE G 190 TRP 0.005 0.001 TRP L 133 HIS 0.003 0.001 HIS H 97 Details of bonding type rmsd covalent geometry : bond 0.00271 (17052) covalent geometry : angle 0.51256 (23316) SS BOND : bond 0.00093 ( 36) SS BOND : angle 0.85108 ( 72) hydrogen bonds : bond 0.03436 ( 1224) hydrogen bonds : angle 3.54452 ( 3636) *********************** 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 398 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 327 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8956 (t70) cc_final: 0.8620 (t0) REVERT: A 133 TRP cc_start: 0.7524 (OUTLIER) cc_final: 0.7314 (m-10) REVERT: A 211 TYR cc_start: 0.8603 (t80) cc_final: 0.8402 (t80) REVERT: A 215 ARG cc_start: 0.8759 (tpp-160) cc_final: 0.8096 (tpt170) REVERT: B 47 GLU cc_start: 0.8768 (pt0) cc_final: 0.8546 (pt0) REVERT: B 66 ASP cc_start: 0.8875 (t70) cc_final: 0.8474 (t0) REVERT: B 133 TRP cc_start: 0.7469 (OUTLIER) cc_final: 0.7230 (m-10) REVERT: B 169 ASP cc_start: 0.8854 (p0) cc_final: 0.8618 (p0) REVERT: B 215 ARG cc_start: 0.8609 (tpp-160) cc_final: 0.8034 (tpt170) REVERT: C 46 ASP cc_start: 0.8880 (p0) cc_final: 0.8593 (p0) REVERT: C 66 ASP cc_start: 0.8939 (t70) cc_final: 0.8612 (t0) REVERT: C 93 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8938 (mmm) REVERT: C 133 TRP cc_start: 0.7516 (OUTLIER) cc_final: 0.7311 (m-10) REVERT: C 203 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9128 (mp) REVERT: C 215 ARG cc_start: 0.8652 (tpp-160) cc_final: 0.8150 (tpt170) REVERT: D 66 ASP cc_start: 0.8961 (t70) cc_final: 0.8625 (t0) REVERT: D 133 TRP cc_start: 0.7476 (OUTLIER) cc_final: 0.7207 (m-10) REVERT: D 211 TYR cc_start: 0.8596 (t80) cc_final: 0.8359 (t80) REVERT: D 215 ARG cc_start: 0.8674 (tpp-160) cc_final: 0.8121 (tpt170) REVERT: E 47 GLU cc_start: 0.8740 (pt0) cc_final: 0.8513 (pt0) REVERT: E 66 ASP cc_start: 0.8894 (t70) cc_final: 0.8493 (t0) REVERT: E 133 TRP cc_start: 0.7468 (OUTLIER) cc_final: 0.7230 (m-10) REVERT: E 142 ARG cc_start: 0.8853 (ttm170) cc_final: 0.8011 (ttm-80) REVERT: E 169 ASP cc_start: 0.8850 (p0) cc_final: 0.8622 (p0) REVERT: E 215 ARG cc_start: 0.8630 (tpp-160) cc_final: 0.8045 (tpt170) REVERT: F 47 GLU cc_start: 0.8752 (pt0) cc_final: 0.8535 (pt0) REVERT: F 66 ASP cc_start: 0.8960 (t70) cc_final: 0.8632 (t0) REVERT: F 93 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.9083 (mmt) REVERT: F 133 TRP cc_start: 0.7473 (OUTLIER) cc_final: 0.7265 (m-10) REVERT: F 203 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9127 (mp) REVERT: F 215 ARG cc_start: 0.8657 (tpp-160) cc_final: 0.8152 (tpt170) REVERT: G 66 ASP cc_start: 0.8953 (t70) cc_final: 0.8624 (t0) REVERT: G 133 TRP cc_start: 0.7481 (OUTLIER) cc_final: 0.7242 (m-10) REVERT: G 211 TYR cc_start: 0.8586 (t80) cc_final: 0.8346 (t80) REVERT: G 215 ARG cc_start: 0.8693 (tpp-160) cc_final: 0.8129 (tpt170) REVERT: H 47 GLU cc_start: 0.8756 (pt0) cc_final: 0.8552 (pt0) REVERT: H 66 ASP cc_start: 0.8906 (t70) cc_final: 0.8498 (t0) REVERT: H 133 TRP cc_start: 0.7465 (OUTLIER) cc_final: 0.7226 (m-10) REVERT: H 146 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8819 (mm-30) REVERT: H 169 ASP cc_start: 0.8913 (p0) cc_final: 0.8692 (p0) REVERT: H 215 ARG cc_start: 0.8640 (tpp-160) cc_final: 0.8042 (tpt170) REVERT: I 47 GLU cc_start: 0.8788 (pt0) cc_final: 0.8585 (pt0) REVERT: I 66 ASP cc_start: 0.8966 (t70) cc_final: 0.8641 (t0) REVERT: I 93 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8952 (mmm) REVERT: I 133 TRP cc_start: 0.7504 (OUTLIER) cc_final: 0.7301 (m-10) REVERT: I 162 MET cc_start: 0.8936 (mmt) cc_final: 0.8680 (mtp) REVERT: I 215 ARG cc_start: 0.8641 (tpp-160) cc_final: 0.8157 (tpt170) REVERT: J 66 ASP cc_start: 0.8975 (t70) cc_final: 0.8644 (t0) REVERT: J 133 TRP cc_start: 0.7482 (OUTLIER) cc_final: 0.7240 (m-10) REVERT: J 211 TYR cc_start: 0.8589 (t80) cc_final: 0.8346 (t80) REVERT: J 215 ARG cc_start: 0.8706 (tpp-160) cc_final: 0.8137 (tpt170) REVERT: K 47 GLU cc_start: 0.8767 (pt0) cc_final: 0.8564 (pt0) REVERT: K 66 ASP cc_start: 0.8894 (t70) cc_final: 0.8491 (t0) REVERT: K 133 TRP cc_start: 0.7434 (OUTLIER) cc_final: 0.7184 (m-10) REVERT: K 146 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8827 (mm-30) REVERT: K 169 ASP cc_start: 0.8893 (p0) cc_final: 0.8663 (p0) REVERT: K 215 ARG cc_start: 0.8655 (tpp-160) cc_final: 0.8044 (tpt170) REVERT: L 47 GLU cc_start: 0.8760 (pt0) cc_final: 0.8555 (pt0) REVERT: L 66 ASP cc_start: 0.8964 (t70) cc_final: 0.8635 (t0) REVERT: L 93 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.8980 (mmm) REVERT: L 162 MET cc_start: 0.8916 (mmt) cc_final: 0.8659 (mtp) REVERT: L 215 ARG cc_start: 0.8657 (tpp-160) cc_final: 0.8167 (tpt170) outliers start: 71 outliers final: 8 residues processed: 367 average time/residue: 0.6373 time to fit residues: 259.9756 Evaluate side-chains 320 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 295 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain B residue 133 TRP 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 E residue 133 TRP Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 133 TRP Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain 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 93 MET Chi-restraints excluded: chain I residue 133 TRP Chi-restraints excluded: chain J residue 133 TRP 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 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 34 optimal weight: 9.9990 chunk 154 optimal weight: 0.6980 chunk 153 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN B 54 ASN B 175 ASN C 54 ASN 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 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.095243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.074438 restraints weight = 31309.360| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.18 r_work: 0.2949 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17088 Z= 0.136 Angle : 0.496 5.268 23388 Z= 0.264 Chirality : 0.042 0.225 2796 Planarity : 0.003 0.022 2784 Dihedral : 3.216 10.620 2232 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.98 % Allowed : 16.99 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.99 (0.17), residues: 2028 helix: 3.18 (0.12), residues: 1404 sheet: 1.07 (0.45), residues: 132 loop : -1.62 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.008 0.001 TYR I 211 PHE 0.009 0.001 PHE G 190 TRP 0.005 0.001 TRP C 133 HIS 0.003 0.001 HIS G 97 Details of bonding type rmsd covalent geometry : bond 0.00318 (17052) covalent geometry : angle 0.49438 (23316) SS BOND : bond 0.00095 ( 36) SS BOND : angle 0.85657 ( 72) hydrogen bonds : bond 0.03167 ( 1224) hydrogen bonds : angle 3.29064 ( 3636) *********************** 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 398 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 324 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.9019 (t70) cc_final: 0.8699 (t0) REVERT: A 93 MET cc_start: 0.9019 (mmt) cc_final: 0.8779 (mmt) REVERT: A 133 TRP cc_start: 0.7482 (OUTLIER) cc_final: 0.7281 (m-10) REVERT: A 211 TYR cc_start: 0.8561 (t80) cc_final: 0.8350 (t80) REVERT: A 215 ARG cc_start: 0.8744 (tpp-160) cc_final: 0.8131 (tpt170) REVERT: B 66 ASP cc_start: 0.8963 (t70) cc_final: 0.8556 (t0) REVERT: B 93 MET cc_start: 0.9370 (tpp) cc_final: 0.9018 (mtp) REVERT: B 133 TRP cc_start: 0.7473 (OUTLIER) cc_final: 0.7259 (m-10) REVERT: B 169 ASP cc_start: 0.8870 (p0) cc_final: 0.8611 (p0) REVERT: B 215 ARG cc_start: 0.8607 (tpp-160) cc_final: 0.8056 (tpt170) REVERT: C 20 ILE cc_start: 0.8580 (mp) cc_final: 0.8239 (mp) REVERT: C 47 GLU cc_start: 0.8781 (pt0) cc_final: 0.8570 (pt0) REVERT: C 66 ASP cc_start: 0.9031 (t70) cc_final: 0.8683 (t0) REVERT: C 203 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9099 (mp) REVERT: C 215 ARG cc_start: 0.8657 (tpp-160) cc_final: 0.8194 (tpt170) REVERT: D 66 ASP cc_start: 0.9006 (t70) cc_final: 0.8671 (t0) REVERT: D 133 TRP cc_start: 0.7413 (OUTLIER) cc_final: 0.7179 (m-10) REVERT: D 211 TYR cc_start: 0.8558 (t80) cc_final: 0.8307 (t80) REVERT: D 215 ARG cc_start: 0.8682 (tpp-160) cc_final: 0.8137 (tpt170) REVERT: E 66 ASP cc_start: 0.8967 (t70) cc_final: 0.8558 (t0) REVERT: E 93 MET cc_start: 0.9393 (tpp) cc_final: 0.9055 (mtp) REVERT: E 133 TRP cc_start: 0.7451 (OUTLIER) cc_final: 0.7232 (m-10) REVERT: E 169 ASP cc_start: 0.8872 (p0) cc_final: 0.8621 (p0) REVERT: E 215 ARG cc_start: 0.8630 (tpp-160) cc_final: 0.8064 (tpt170) REVERT: F 46 ASP cc_start: 0.8938 (p0) cc_final: 0.8619 (p0) REVERT: F 66 ASP cc_start: 0.9020 (t70) cc_final: 0.8671 (t0) REVERT: F 93 MET cc_start: 0.9406 (OUTLIER) cc_final: 0.8986 (mmm) REVERT: F 133 TRP cc_start: 0.7495 (OUTLIER) cc_final: 0.7285 (m-10) REVERT: F 167 LYS cc_start: 0.9216 (mptm) cc_final: 0.9006 (mmtt) REVERT: F 203 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9089 (mp) REVERT: F 215 ARG cc_start: 0.8678 (tpp-160) cc_final: 0.8196 (tpt170) REVERT: G 66 ASP cc_start: 0.9012 (t70) cc_final: 0.8683 (t0) REVERT: G 133 TRP cc_start: 0.7431 (OUTLIER) cc_final: 0.7195 (m-10) REVERT: G 211 TYR cc_start: 0.8570 (t80) cc_final: 0.8310 (t80) REVERT: G 215 ARG cc_start: 0.8679 (tpp-160) cc_final: 0.8142 (tpt170) REVERT: H 66 ASP cc_start: 0.8976 (t70) cc_final: 0.8529 (t0) REVERT: H 133 TRP cc_start: 0.7481 (OUTLIER) cc_final: 0.7243 (m-10) REVERT: H 169 ASP cc_start: 0.8940 (p0) cc_final: 0.8678 (p0) REVERT: H 215 ARG cc_start: 0.8657 (tpp-160) cc_final: 0.8067 (tpt170) REVERT: I 20 ILE cc_start: 0.8615 (mp) cc_final: 0.8281 (mp) REVERT: I 46 ASP cc_start: 0.8956 (p0) cc_final: 0.8669 (p0) REVERT: I 66 ASP cc_start: 0.9017 (t70) cc_final: 0.8659 (t0) REVERT: I 93 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8976 (mmm) REVERT: I 133 TRP cc_start: 0.7496 (OUTLIER) cc_final: 0.7294 (m-10) REVERT: I 215 ARG cc_start: 0.8659 (tpp-160) cc_final: 0.8180 (tpt170) REVERT: J 66 ASP cc_start: 0.9024 (t70) cc_final: 0.8689 (t0) REVERT: J 133 TRP cc_start: 0.7458 (OUTLIER) cc_final: 0.7250 (m-10) REVERT: J 211 TYR cc_start: 0.8570 (t80) cc_final: 0.8312 (t80) REVERT: J 215 ARG cc_start: 0.8716 (tpp-160) cc_final: 0.8136 (tpt170) REVERT: K 66 ASP cc_start: 0.8970 (t70) cc_final: 0.8520 (t0) REVERT: K 133 TRP cc_start: 0.7447 (OUTLIER) cc_final: 0.7206 (m-10) REVERT: K 169 ASP cc_start: 0.8920 (p0) cc_final: 0.8663 (p0) REVERT: K 215 ARG cc_start: 0.8636 (tpp-160) cc_final: 0.8054 (tpt170) REVERT: L 20 ILE cc_start: 0.8604 (mp) cc_final: 0.8265 (mp) REVERT: L 46 ASP cc_start: 0.8927 (p0) cc_final: 0.8632 (p0) REVERT: L 66 ASP cc_start: 0.9028 (t70) cc_final: 0.8670 (t0) REVERT: L 93 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.8989 (mmt) REVERT: L 167 LYS cc_start: 0.9233 (mptm) cc_final: 0.9028 (mmtt) REVERT: L 215 ARG cc_start: 0.8644 (tpp-160) cc_final: 0.8179 (tpt170) outliers start: 74 outliers final: 13 residues processed: 362 average time/residue: 0.6259 time to fit residues: 252.2958 Evaluate side-chains 318 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 290 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 203 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 133 TRP Chi-restraints excluded: chain F residue 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 89 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.071826 restraints weight = 31487.258| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.19 r_work: 0.2884 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 17088 Z= 0.206 Angle : 0.532 5.360 23388 Z= 0.281 Chirality : 0.044 0.232 2796 Planarity : 0.003 0.022 2784 Dihedral : 3.309 12.124 2232 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.11 % Allowed : 17.47 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.17), residues: 2028 helix: 3.09 (0.12), residues: 1404 sheet: 1.30 (0.46), residues: 132 loop : -1.55 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 32 TYR 0.011 0.001 TYR A 65 PHE 0.014 0.002 PHE F 68 TRP 0.009 0.001 TRP H 44 HIS 0.005 0.001 HIS L 73 Details of bonding type rmsd covalent geometry : bond 0.00483 (17052) covalent geometry : angle 0.53022 (23316) SS BOND : bond 0.00231 ( 36) SS BOND : angle 1.01597 ( 72) hydrogen bonds : bond 0.03119 ( 1224) hydrogen bonds : angle 3.22696 ( 3636) *********************** 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 414 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 319 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.9183 (t70) cc_final: 0.8857 (t0) REVERT: A 133 TRP cc_start: 0.7474 (OUTLIER) cc_final: 0.7262 (m-10) REVERT: A 169 ASP cc_start: 0.8768 (p0) cc_final: 0.8495 (p0) REVERT: A 211 TYR cc_start: 0.8575 (t80) cc_final: 0.8372 (t80) REVERT: A 215 ARG cc_start: 0.8716 (tpp-160) cc_final: 0.8141 (tpt170) REVERT: B 66 ASP cc_start: 0.9121 (t70) cc_final: 0.8730 (t0) REVERT: B 93 MET cc_start: 0.9396 (tpp) cc_final: 0.9037 (mtp) REVERT: B 97 HIS cc_start: 0.8149 (OUTLIER) cc_final: 0.7230 (t70) REVERT: B 133 TRP cc_start: 0.7460 (OUTLIER) cc_final: 0.7251 (m-10) REVERT: B 169 ASP cc_start: 0.8847 (p0) cc_final: 0.8575 (p0) REVERT: B 215 ARG cc_start: 0.8588 (tpp-160) cc_final: 0.8073 (tpt170) REVERT: C 20 ILE cc_start: 0.8642 (mp) cc_final: 0.8341 (mp) REVERT: C 46 ASP cc_start: 0.8945 (p0) cc_final: 0.8680 (p0) REVERT: C 66 ASP cc_start: 0.9159 (t70) cc_final: 0.8749 (t0) REVERT: C 133 TRP cc_start: 0.7548 (m-10) cc_final: 0.7281 (m-10) REVERT: C 203 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9132 (mp) REVERT: C 215 ARG cc_start: 0.8615 (tpp-160) cc_final: 0.8174 (tpt170) REVERT: D 66 ASP cc_start: 0.9161 (t70) cc_final: 0.8831 (t0) REVERT: D 133 TRP cc_start: 0.7423 (OUTLIER) cc_final: 0.7193 (m-10) REVERT: D 211 TYR cc_start: 0.8564 (t80) cc_final: 0.8317 (t80) REVERT: D 215 ARG cc_start: 0.8662 (tpp-160) cc_final: 0.8137 (tpt170) REVERT: E 66 ASP cc_start: 0.9130 (t70) cc_final: 0.8742 (t0) REVERT: E 93 MET cc_start: 0.9404 (tpp) cc_final: 0.9050 (mtp) REVERT: E 97 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7257 (t70) REVERT: E 133 TRP cc_start: 0.7440 (OUTLIER) cc_final: 0.7228 (m-10) REVERT: E 169 ASP cc_start: 0.8867 (p0) cc_final: 0.8604 (p0) REVERT: E 215 ARG cc_start: 0.8585 (tpp-160) cc_final: 0.8082 (tpt170) REVERT: F 46 ASP cc_start: 0.8910 (p0) cc_final: 0.8615 (p0) REVERT: F 66 ASP cc_start: 0.9152 (t70) cc_final: 0.8739 (t0) REVERT: F 93 MET cc_start: 0.9432 (OUTLIER) cc_final: 0.9022 (mmm) REVERT: F 133 TRP cc_start: 0.7471 (OUTLIER) cc_final: 0.7266 (m-10) REVERT: F 167 LYS cc_start: 0.9252 (mptm) cc_final: 0.9042 (mmtt) REVERT: F 203 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9128 (mp) REVERT: F 215 ARG cc_start: 0.8644 (tpp-160) cc_final: 0.8200 (tpt170) REVERT: G 66 ASP cc_start: 0.9164 (t70) cc_final: 0.8837 (t0) REVERT: G 133 TRP cc_start: 0.7435 (OUTLIER) cc_final: 0.7203 (m-10) REVERT: G 211 TYR cc_start: 0.8547 (t80) cc_final: 0.8295 (t80) REVERT: G 215 ARG cc_start: 0.8647 (tpp-160) cc_final: 0.8138 (tpt170) REVERT: H 66 ASP cc_start: 0.9126 (t70) cc_final: 0.8736 (t0) REVERT: H 93 MET cc_start: 0.9418 (tpp) cc_final: 0.9062 (mtp) REVERT: H 97 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7214 (t70) REVERT: H 133 TRP cc_start: 0.7475 (OUTLIER) cc_final: 0.7241 (m-10) REVERT: H 169 ASP cc_start: 0.8893 (p0) cc_final: 0.8616 (p0) REVERT: H 215 ARG cc_start: 0.8622 (tpp-160) cc_final: 0.8083 (tpt170) REVERT: I 20 ILE cc_start: 0.8648 (mp) cc_final: 0.8362 (mp) REVERT: I 46 ASP cc_start: 0.8917 (p0) cc_final: 0.8619 (p0) REVERT: I 66 ASP cc_start: 0.9146 (t70) cc_final: 0.8736 (t0) REVERT: I 133 TRP cc_start: 0.7464 (OUTLIER) cc_final: 0.7262 (m-10) REVERT: I 215 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8155 (tpt170) REVERT: J 66 ASP cc_start: 0.9179 (t70) cc_final: 0.8847 (t0) REVERT: J 133 TRP cc_start: 0.7464 (OUTLIER) cc_final: 0.7260 (m-10) REVERT: J 211 TYR cc_start: 0.8548 (t80) cc_final: 0.8300 (t80) REVERT: J 215 ARG cc_start: 0.8664 (tpp-160) cc_final: 0.8130 (tpt170) REVERT: K 66 ASP cc_start: 0.9125 (t70) cc_final: 0.8733 (t0) REVERT: K 93 MET cc_start: 0.9400 (tpp) cc_final: 0.9037 (mtp) REVERT: K 97 HIS cc_start: 0.8129 (OUTLIER) cc_final: 0.7229 (t70) REVERT: K 133 TRP cc_start: 0.7446 (OUTLIER) cc_final: 0.7209 (m-10) REVERT: K 169 ASP cc_start: 0.8892 (p0) cc_final: 0.8619 (p0) REVERT: K 215 ARG cc_start: 0.8600 (tpp-160) cc_final: 0.8086 (tpt170) REVERT: L 20 ILE cc_start: 0.8648 (mp) cc_final: 0.8362 (mp) REVERT: L 46 ASP cc_start: 0.8905 (p0) cc_final: 0.8621 (p0) REVERT: L 66 ASP cc_start: 0.9160 (t70) cc_final: 0.8752 (t0) REVERT: L 93 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.9084 (mmm) REVERT: L 133 TRP cc_start: 0.7537 (m-10) cc_final: 0.7251 (m-10) REVERT: L 167 LYS cc_start: 0.9280 (mptm) cc_final: 0.9073 (mmtt) REVERT: L 215 ARG cc_start: 0.8628 (tpp-160) cc_final: 0.8166 (tpt170) outliers start: 95 outliers final: 29 residues processed: 378 average time/residue: 0.6107 time to fit residues: 257.6357 Evaluate side-chains 324 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 277 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 HIS 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 86 THR 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 D residue 134 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 133 TRP Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 133 TRP Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 133 TRP Chi-restraints excluded: chain J residue 86 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 86 THR Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 133 TRP Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 214 ILE Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 25 optimal weight: 0.1980 chunk 185 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN B 54 ASN B 97 HIS B 175 ASN C 54 ASN C 175 ASN D 54 ASN D 97 HIS D 175 ASN E 54 ASN E 97 HIS E 175 ASN F 54 ASN F 97 HIS F 175 ASN G 54 ASN G 97 HIS G 175 ASN H 54 ASN H 97 HIS H 175 ASN I 54 ASN I 175 ASN J 54 ASN J 175 ASN K 54 ASN K 97 HIS K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.093650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.072331 restraints weight = 31345.676| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.18 r_work: 0.2896 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17088 Z= 0.161 Angle : 0.505 5.284 23388 Z= 0.269 Chirality : 0.043 0.254 2796 Planarity : 0.003 0.028 2784 Dihedral : 3.303 11.856 2232 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.27 % Allowed : 18.01 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.92 (0.17), residues: 2028 helix: 3.07 (0.12), residues: 1404 sheet: 1.32 (0.46), residues: 132 loop : -1.53 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 22 TYR 0.010 0.001 TYR B 65 PHE 0.010 0.001 PHE H 180 TRP 0.006 0.001 TRP C 44 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00378 (17052) covalent geometry : angle 0.50363 (23316) SS BOND : bond 0.00192 ( 36) SS BOND : angle 0.80669 ( 72) hydrogen bonds : bond 0.02981 ( 1224) hydrogen bonds : angle 3.20727 ( 3636) *********************** 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 410 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 312 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.9166 (t70) cc_final: 0.8826 (t0) REVERT: A 133 TRP cc_start: 0.7430 (OUTLIER) cc_final: 0.7230 (m-10) REVERT: A 169 ASP cc_start: 0.8751 (p0) cc_final: 0.8513 (p0) REVERT: A 211 TYR cc_start: 0.8575 (t80) cc_final: 0.8362 (t80) REVERT: A 215 ARG cc_start: 0.8718 (tpp-160) cc_final: 0.8137 (tpt170) REVERT: B 66 ASP cc_start: 0.9122 (t70) cc_final: 0.8727 (t0) REVERT: B 133 TRP cc_start: 0.7434 (OUTLIER) cc_final: 0.7231 (m-10) REVERT: B 169 ASP cc_start: 0.8790 (p0) cc_final: 0.8518 (p0) REVERT: B 215 ARG cc_start: 0.8596 (tpp-160) cc_final: 0.8067 (tpt170) REVERT: C 20 ILE cc_start: 0.8624 (mp) cc_final: 0.8342 (mp) REVERT: C 46 ASP cc_start: 0.8937 (p0) cc_final: 0.8650 (p0) REVERT: C 66 ASP cc_start: 0.9164 (t70) cc_final: 0.8745 (t0) REVERT: C 133 TRP cc_start: 0.7514 (m-10) cc_final: 0.7210 (m-10) REVERT: C 203 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9112 (mp) REVERT: C 215 ARG cc_start: 0.8614 (tpp-160) cc_final: 0.8193 (tpt170) REVERT: D 66 ASP cc_start: 0.9137 (t70) cc_final: 0.8790 (t0) REVERT: D 133 TRP cc_start: 0.7373 (OUTLIER) cc_final: 0.7149 (m-10) REVERT: D 211 TYR cc_start: 0.8552 (t80) cc_final: 0.8301 (t80) REVERT: D 215 ARG cc_start: 0.8665 (tpp-160) cc_final: 0.8152 (tpt170) REVERT: E 66 ASP cc_start: 0.9127 (t70) cc_final: 0.8733 (t0) REVERT: E 133 TRP cc_start: 0.7422 (OUTLIER) cc_final: 0.7216 (m-10) REVERT: E 169 ASP cc_start: 0.8819 (p0) cc_final: 0.8564 (p0) REVERT: E 215 ARG cc_start: 0.8592 (tpp-160) cc_final: 0.8074 (tpt170) REVERT: F 46 ASP cc_start: 0.8894 (p0) cc_final: 0.8596 (p0) REVERT: F 66 ASP cc_start: 0.9154 (t70) cc_final: 0.8731 (t0) REVERT: F 93 MET cc_start: 0.9442 (OUTLIER) cc_final: 0.9193 (mmt) REVERT: F 167 LYS cc_start: 0.9221 (mptm) cc_final: 0.9017 (mmtt) REVERT: F 203 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9106 (mp) REVERT: F 215 ARG cc_start: 0.8609 (tpp-160) cc_final: 0.8182 (tpt170) REVERT: G 66 ASP cc_start: 0.9150 (t70) cc_final: 0.8806 (t0) REVERT: G 133 TRP cc_start: 0.7370 (OUTLIER) cc_final: 0.7143 (m-10) REVERT: G 211 TYR cc_start: 0.8540 (t80) cc_final: 0.8306 (t80) REVERT: G 215 ARG cc_start: 0.8666 (tpp-160) cc_final: 0.8148 (tpt170) REVERT: H 66 ASP cc_start: 0.9135 (t70) cc_final: 0.8735 (t0) REVERT: H 133 TRP cc_start: 0.7404 (OUTLIER) cc_final: 0.7172 (m-10) REVERT: H 169 ASP cc_start: 0.8849 (p0) cc_final: 0.8597 (p0) REVERT: H 215 ARG cc_start: 0.8581 (tpp-160) cc_final: 0.8064 (tpt170) REVERT: I 20 ILE cc_start: 0.8638 (mp) cc_final: 0.8371 (mp) REVERT: I 46 ASP cc_start: 0.8921 (p0) cc_final: 0.8621 (p0) REVERT: I 66 ASP cc_start: 0.9158 (t70) cc_final: 0.8741 (t0) REVERT: I 215 ARG cc_start: 0.8599 (tpp-160) cc_final: 0.8179 (tpt170) REVERT: J 22 ARG cc_start: 0.7265 (ttt180) cc_final: 0.7039 (ttm110) REVERT: J 66 ASP cc_start: 0.9164 (t70) cc_final: 0.8820 (t0) REVERT: J 133 TRP cc_start: 0.7367 (OUTLIER) cc_final: 0.7164 (m-10) REVERT: J 211 TYR cc_start: 0.8566 (t80) cc_final: 0.8303 (t80) REVERT: J 215 ARG cc_start: 0.8663 (tpp-160) cc_final: 0.8127 (tpt170) REVERT: K 66 ASP cc_start: 0.9131 (t70) cc_final: 0.8729 (t0) REVERT: K 133 TRP cc_start: 0.7407 (OUTLIER) cc_final: 0.7206 (m-10) REVERT: K 169 ASP cc_start: 0.8834 (p0) cc_final: 0.8578 (p0) REVERT: K 215 ARG cc_start: 0.8603 (tpp-160) cc_final: 0.8063 (tpt170) REVERT: L 20 ILE cc_start: 0.8639 (mp) cc_final: 0.8369 (mp) REVERT: L 46 ASP cc_start: 0.8898 (p0) cc_final: 0.8596 (p0) REVERT: L 66 ASP cc_start: 0.9169 (t70) cc_final: 0.8754 (t0) REVERT: L 93 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.9063 (mmm) REVERT: L 133 TRP cc_start: 0.7503 (m100) cc_final: 0.7196 (m-10) REVERT: L 215 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8182 (tpt170) outliers start: 98 outliers final: 33 residues processed: 376 average time/residue: 0.6108 time to fit residues: 256.0056 Evaluate side-chains 326 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 133 TRP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 133 TRP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 133 TRP Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 214 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 86 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 86 THR Chi-restraints excluded: chain K residue 133 TRP Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 86 THR 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 52 optimal weight: 0.7980 chunk 168 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN B 54 ASN B 97 HIS B 175 ASN C 54 ASN C 175 ASN D 54 ASN D 97 HIS D 175 ASN E 54 ASN E 97 HIS E 175 ASN F 54 ASN F 97 HIS F 175 ASN G 54 ASN G 97 HIS G 175 ASN H 54 ASN H 97 HIS H 175 ASN I 54 ASN I 97 HIS I 175 ASN J 54 ASN J 175 ASN K 54 ASN K 97 HIS K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.095092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.073878 restraints weight = 31148.161| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.19 r_work: 0.2924 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17088 Z= 0.113 Angle : 0.470 5.184 23388 Z= 0.249 Chirality : 0.041 0.242 2796 Planarity : 0.003 0.022 2784 Dihedral : 3.242 10.796 2232 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.95 % Allowed : 19.35 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.02 (0.17), residues: 2028 helix: 3.17 (0.12), residues: 1404 sheet: 1.23 (0.47), residues: 132 loop : -1.53 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 75 TYR 0.008 0.001 TYR E 65 PHE 0.011 0.001 PHE B 180 TRP 0.005 0.001 TRP H 44 HIS 0.004 0.000 HIS I 97 Details of bonding type rmsd covalent geometry : bond 0.00259 (17052) covalent geometry : angle 0.46956 (23316) SS BOND : bond 0.00157 ( 36) SS BOND : angle 0.62607 ( 72) hydrogen bonds : bond 0.02844 ( 1224) hydrogen bonds : angle 3.12836 ( 3636) *********************** 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 421 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 329 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.9115 (t70) cc_final: 0.8795 (t0) REVERT: A 133 TRP cc_start: 0.7387 (OUTLIER) cc_final: 0.7186 (m-10) REVERT: A 211 TYR cc_start: 0.8584 (t80) cc_final: 0.8360 (t80) REVERT: A 215 ARG cc_start: 0.8693 (tpp-160) cc_final: 0.8112 (tpt170) REVERT: B 66 ASP cc_start: 0.9080 (t70) cc_final: 0.8687 (t0) REVERT: B 133 TRP cc_start: 0.7363 (OUTLIER) cc_final: 0.7155 (m-10) REVERT: B 169 ASP cc_start: 0.8705 (p0) cc_final: 0.8469 (p0) REVERT: B 215 ARG cc_start: 0.8610 (tpp-160) cc_final: 0.8085 (tpt170) REVERT: C 20 ILE cc_start: 0.8573 (mp) cc_final: 0.8310 (mp) REVERT: C 46 ASP cc_start: 0.8886 (p0) cc_final: 0.8600 (p0) REVERT: C 66 ASP cc_start: 0.9115 (t70) cc_final: 0.8723 (t0) REVERT: C 133 TRP cc_start: 0.7457 (m-10) cc_final: 0.7134 (m-10) REVERT: C 203 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9097 (mp) REVERT: C 215 ARG cc_start: 0.8591 (tpp-160) cc_final: 0.8190 (tpt170) REVERT: D 66 ASP cc_start: 0.9092 (t70) cc_final: 0.8761 (t0) REVERT: D 133 TRP cc_start: 0.7339 (OUTLIER) cc_final: 0.7138 (m-10) REVERT: D 169 ASP cc_start: 0.8751 (p0) cc_final: 0.8539 (p0) REVERT: D 211 TYR cc_start: 0.8577 (t80) cc_final: 0.8305 (t80) REVERT: D 215 ARG cc_start: 0.8682 (tpp-160) cc_final: 0.8143 (tpt170) REVERT: E 66 ASP cc_start: 0.9090 (t70) cc_final: 0.8697 (t0) REVERT: E 133 TRP cc_start: 0.7341 (OUTLIER) cc_final: 0.7130 (m-10) REVERT: E 169 ASP cc_start: 0.8754 (p0) cc_final: 0.8530 (p0) REVERT: E 215 ARG cc_start: 0.8597 (tpp-160) cc_final: 0.8080 (tpt170) REVERT: F 46 ASP cc_start: 0.8857 (p0) cc_final: 0.8567 (p0) REVERT: F 66 ASP cc_start: 0.9103 (t70) cc_final: 0.8719 (t0) REVERT: F 93 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.8812 (mmm) REVERT: F 203 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9095 (mp) REVERT: F 215 ARG cc_start: 0.8604 (tpp-160) cc_final: 0.8203 (tpt170) REVERT: G 66 ASP cc_start: 0.9104 (t70) cc_final: 0.8775 (t0) REVERT: G 211 TYR cc_start: 0.8555 (t80) cc_final: 0.8281 (t80) REVERT: G 215 ARG cc_start: 0.8659 (tpp-160) cc_final: 0.8138 (tpt170) REVERT: H 66 ASP cc_start: 0.9096 (t70) cc_final: 0.8691 (t0) REVERT: H 133 TRP cc_start: 0.7330 (OUTLIER) cc_final: 0.7124 (m-10) REVERT: H 169 ASP cc_start: 0.8762 (p0) cc_final: 0.8540 (p0) REVERT: H 215 ARG cc_start: 0.8601 (tpp-160) cc_final: 0.8086 (tpt170) REVERT: I 20 ILE cc_start: 0.8613 (mp) cc_final: 0.8355 (mp) REVERT: I 66 ASP cc_start: 0.9107 (t70) cc_final: 0.8718 (t0) REVERT: I 215 ARG cc_start: 0.8553 (tpp-160) cc_final: 0.8162 (tpt170) REVERT: J 66 ASP cc_start: 0.9117 (t70) cc_final: 0.8789 (t0) REVERT: J 133 TRP cc_start: 0.7350 (OUTLIER) cc_final: 0.7141 (m-10) REVERT: J 211 TYR cc_start: 0.8573 (t80) cc_final: 0.8325 (t80) REVERT: J 215 ARG cc_start: 0.8636 (tpp-160) cc_final: 0.8139 (tpt170) REVERT: K 66 ASP cc_start: 0.9090 (t70) cc_final: 0.8684 (t0) REVERT: K 133 TRP cc_start: 0.7337 (OUTLIER) cc_final: 0.7132 (m-10) REVERT: K 169 ASP cc_start: 0.8756 (p0) cc_final: 0.8530 (p0) REVERT: K 215 ARG cc_start: 0.8610 (tpp-160) cc_final: 0.8092 (tpt170) REVERT: L 20 ILE cc_start: 0.8617 (mp) cc_final: 0.8354 (mp) REVERT: L 66 ASP cc_start: 0.9123 (t70) cc_final: 0.8734 (t0) REVERT: L 93 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.8955 (mmm) REVERT: L 133 TRP cc_start: 0.7453 (m100) cc_final: 0.7148 (m-10) REVERT: L 215 ARG cc_start: 0.8564 (tpp-160) cc_final: 0.8172 (tpt170) outliers start: 92 outliers final: 17 residues processed: 384 average time/residue: 0.6029 time to fit residues: 258.4583 Evaluate side-chains 318 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 290 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 133 TRP 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 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 E residue 214 ILE 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 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 60 CYS 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 60 CYS Chi-restraints excluded: chain L residue 93 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 10 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 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 G 205 ASN H 54 ASN H 97 HIS H 175 ASN I 54 ASN I 97 HIS I 175 ASN J 54 ASN J 175 ASN J 205 ASN K 54 ASN K 97 HIS K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.073327 restraints weight = 31072.525| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.20 r_work: 0.2907 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17088 Z= 0.144 Angle : 0.501 5.458 23388 Z= 0.267 Chirality : 0.042 0.261 2796 Planarity : 0.003 0.024 2784 Dihedral : 3.242 12.225 2232 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.16 % Allowed : 19.46 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.04 (0.17), residues: 2028 helix: 3.16 (0.12), residues: 1404 sheet: 1.30 (0.47), residues: 132 loop : -1.45 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 32 TYR 0.009 0.001 TYR E 65 PHE 0.010 0.001 PHE B 180 TRP 0.006 0.001 TRP D 44 HIS 0.002 0.000 HIS I 73 Details of bonding type rmsd covalent geometry : bond 0.00336 (17052) covalent geometry : angle 0.50001 (23316) SS BOND : bond 0.00171 ( 36) SS BOND : angle 0.68750 ( 72) hydrogen bonds : bond 0.02853 ( 1224) hydrogen bonds : angle 3.11231 ( 3636) *********************** 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 392 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 296 time to evaluate : 0.641 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 66 ASP cc_start: 0.9139 (t70) cc_final: 0.8805 (t0) REVERT: A 211 TYR cc_start: 0.8596 (t80) cc_final: 0.8354 (t80) REVERT: A 215 ARG cc_start: 0.8689 (tpp-160) cc_final: 0.8121 (tpt170) REVERT: B 66 ASP cc_start: 0.9111 (t70) cc_final: 0.8721 (t0) REVERT: B 169 ASP cc_start: 0.8723 (p0) cc_final: 0.8475 (p0) REVERT: B 215 ARG cc_start: 0.8629 (tpp-160) cc_final: 0.8078 (tpt170) REVERT: C 46 ASP cc_start: 0.8895 (p0) cc_final: 0.8607 (p0) REVERT: C 66 ASP cc_start: 0.9142 (t70) cc_final: 0.8755 (t0) REVERT: C 133 TRP cc_start: 0.7453 (m-10) cc_final: 0.7139 (m-10) REVERT: C 203 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9099 (mp) REVERT: C 215 ARG cc_start: 0.8601 (tpp-160) cc_final: 0.8189 (tpt170) REVERT: D 66 ASP cc_start: 0.9127 (t70) cc_final: 0.8796 (t0) REVERT: D 169 ASP cc_start: 0.8727 (p0) cc_final: 0.8465 (p0) REVERT: D 211 TYR cc_start: 0.8560 (t80) cc_final: 0.8272 (t80) REVERT: D 215 ARG cc_start: 0.8647 (tpp-160) cc_final: 0.8144 (tpt170) REVERT: E 66 ASP cc_start: 0.9121 (t70) cc_final: 0.8731 (t0) REVERT: E 133 TRP cc_start: 0.7344 (OUTLIER) cc_final: 0.7141 (m-10) REVERT: E 169 ASP cc_start: 0.8769 (p0) cc_final: 0.8529 (p0) REVERT: E 215 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8082 (tpt170) REVERT: F 66 ASP cc_start: 0.9137 (t70) cc_final: 0.8748 (t0) REVERT: F 93 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.8805 (mmm) REVERT: F 203 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9093 (mp) REVERT: F 215 ARG cc_start: 0.8604 (tpp-160) cc_final: 0.8191 (tpt170) REVERT: G 66 ASP cc_start: 0.9129 (t70) cc_final: 0.8796 (t0) REVERT: G 211 TYR cc_start: 0.8550 (t80) cc_final: 0.8299 (t80) REVERT: G 215 ARG cc_start: 0.8663 (tpp-160) cc_final: 0.8147 (tpt170) REVERT: H 66 ASP cc_start: 0.9128 (t70) cc_final: 0.8739 (t0) REVERT: H 169 ASP cc_start: 0.8765 (p0) cc_final: 0.8542 (p0) REVERT: H 215 ARG cc_start: 0.8615 (tpp-160) cc_final: 0.8074 (tpt170) REVERT: I 20 ILE cc_start: 0.8634 (mp) cc_final: 0.8391 (mp) REVERT: I 66 ASP cc_start: 0.9132 (t70) cc_final: 0.8745 (t0) REVERT: I 215 ARG cc_start: 0.8585 (tpp-160) cc_final: 0.8174 (tpt170) REVERT: J 66 ASP cc_start: 0.9134 (t70) cc_final: 0.8805 (t0) REVERT: J 133 TRP cc_start: 0.7338 (OUTLIER) cc_final: 0.7135 (m-10) REVERT: J 169 ASP cc_start: 0.8770 (p0) cc_final: 0.8566 (p0) REVERT: J 211 TYR cc_start: 0.8563 (t80) cc_final: 0.8309 (t80) REVERT: J 215 ARG cc_start: 0.8657 (tpp-160) cc_final: 0.8150 (tpt170) REVERT: K 66 ASP cc_start: 0.9117 (t70) cc_final: 0.8726 (t0) REVERT: K 169 ASP cc_start: 0.8749 (p0) cc_final: 0.8518 (p0) REVERT: K 215 ARG cc_start: 0.8621 (tpp-160) cc_final: 0.8080 (tpt170) REVERT: L 20 ILE cc_start: 0.8636 (mp) cc_final: 0.8393 (mp) REVERT: L 93 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.8977 (mmm) REVERT: L 133 TRP cc_start: 0.7450 (m100) cc_final: 0.7073 (m-10) REVERT: L 215 ARG cc_start: 0.8587 (tpp-160) cc_final: 0.8177 (tpt170) outliers start: 96 outliers final: 23 residues processed: 356 average time/residue: 0.5308 time to fit residues: 211.4771 Evaluate side-chains 311 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 282 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 71 ILE 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 133 TRP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 60 CYS Chi-restraints excluded: chain F residue 71 ILE 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 H residue 150 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 156 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 195 optimal weight: 20.0000 chunk 150 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 175 ASN B 54 ASN B 97 HIS B 175 ASN C 54 ASN C 175 ASN D 54 ASN D 97 HIS D 175 ASN E 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 97 HIS 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: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.073308 restraints weight = 31208.391| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.21 r_work: 0.2909 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17088 Z= 0.148 Angle : 0.510 5.690 23388 Z= 0.272 Chirality : 0.042 0.245 2796 Planarity : 0.003 0.025 2784 Dihedral : 3.261 13.016 2232 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.19 % Allowed : 20.22 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.04 (0.17), residues: 2028 helix: 3.14 (0.12), residues: 1404 sheet: 1.33 (0.48), residues: 132 loop : -1.39 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 32 TYR 0.010 0.001 TYR B 65 PHE 0.009 0.001 PHE I 68 TRP 0.006 0.001 TRP J 44 HIS 0.003 0.000 HIS L 97 Details of bonding type rmsd covalent geometry : bond 0.00348 (17052) covalent geometry : angle 0.50895 (23316) SS BOND : bond 0.00171 ( 36) SS BOND : angle 0.69031 ( 72) hydrogen bonds : bond 0.02867 ( 1224) hydrogen bonds : angle 3.13909 ( 3636) *********************** 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 365 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 287 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.9168 (t70) cc_final: 0.8820 (t0) REVERT: A 211 TYR cc_start: 0.8564 (t80) cc_final: 0.8312 (t80) REVERT: A 215 ARG cc_start: 0.8708 (tpp-160) cc_final: 0.8118 (tpt170) REVERT: B 66 ASP cc_start: 0.9138 (t70) cc_final: 0.8742 (t0) REVERT: B 80 GLN cc_start: 0.9400 (tt0) cc_final: 0.9182 (tt0) REVERT: B 169 ASP cc_start: 0.8724 (p0) cc_final: 0.8489 (p0) REVERT: B 215 ARG cc_start: 0.8655 (tpp-160) cc_final: 0.8079 (tpt170) REVERT: C 20 ILE cc_start: 0.8545 (mp) cc_final: 0.8329 (mp) REVERT: C 46 ASP cc_start: 0.8898 (p0) cc_final: 0.8623 (p0) REVERT: C 133 TRP cc_start: 0.7428 (m-10) cc_final: 0.7110 (m-10) REVERT: C 203 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9071 (mp) REVERT: C 215 ARG cc_start: 0.8620 (tpp-160) cc_final: 0.8178 (tpt170) REVERT: D 66 ASP cc_start: 0.9145 (t70) cc_final: 0.8786 (t0) REVERT: D 169 ASP cc_start: 0.8725 (p0) cc_final: 0.8449 (p0) REVERT: D 211 TYR cc_start: 0.8539 (t80) cc_final: 0.8277 (t80) REVERT: D 215 ARG cc_start: 0.8674 (tpp-160) cc_final: 0.8145 (tpt170) REVERT: E 66 ASP cc_start: 0.9148 (t70) cc_final: 0.8747 (t0) REVERT: E 169 ASP cc_start: 0.8764 (p0) cc_final: 0.8537 (p0) REVERT: E 215 ARG cc_start: 0.8645 (tpp-160) cc_final: 0.8079 (tpt170) REVERT: F 93 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.9089 (mmt) REVERT: F 203 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9063 (mp) REVERT: F 215 ARG cc_start: 0.8623 (tpp-160) cc_final: 0.8191 (tpt170) REVERT: G 66 ASP cc_start: 0.9156 (t70) cc_final: 0.8797 (t0) REVERT: G 211 TYR cc_start: 0.8540 (t80) cc_final: 0.8286 (t80) REVERT: G 215 ARG cc_start: 0.8680 (tpp-160) cc_final: 0.8149 (tpt170) REVERT: H 66 ASP cc_start: 0.9141 (t70) cc_final: 0.8740 (t0) REVERT: H 93 MET cc_start: 0.9405 (tpp) cc_final: 0.9096 (mtp) REVERT: H 169 ASP cc_start: 0.8747 (p0) cc_final: 0.8542 (p0) REVERT: H 215 ARG cc_start: 0.8631 (tpp-160) cc_final: 0.8069 (tpt170) REVERT: I 20 ILE cc_start: 0.8605 (mp) cc_final: 0.8385 (mp) REVERT: I 215 ARG cc_start: 0.8596 (tpp-160) cc_final: 0.8165 (tpt170) REVERT: J 66 ASP cc_start: 0.9156 (t70) cc_final: 0.8797 (t0) REVERT: J 169 ASP cc_start: 0.8761 (p0) cc_final: 0.8508 (p0) REVERT: J 211 TYR cc_start: 0.8543 (t80) cc_final: 0.8273 (t80) REVERT: J 215 ARG cc_start: 0.8682 (tpp-160) cc_final: 0.8164 (tpt170) REVERT: K 66 ASP cc_start: 0.9141 (t70) cc_final: 0.8741 (t0) REVERT: K 93 MET cc_start: 0.9403 (tpp) cc_final: 0.9090 (mtp) REVERT: K 169 ASP cc_start: 0.8727 (p0) cc_final: 0.8515 (p0) REVERT: K 215 ARG cc_start: 0.8652 (tpp-160) cc_final: 0.8078 (tpt170) REVERT: L 20 ILE cc_start: 0.8615 (mp) cc_final: 0.8389 (mp) REVERT: L 93 MET cc_start: 0.9354 (OUTLIER) cc_final: 0.8953 (mmm) REVERT: L 133 TRP cc_start: 0.7440 (m100) cc_final: 0.7058 (m-10) REVERT: L 215 ARG cc_start: 0.8600 (tpp-160) cc_final: 0.8165 (tpt170) outliers start: 78 outliers final: 24 residues processed: 337 average time/residue: 0.5769 time to fit residues: 217.5125 Evaluate side-chains 305 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 71 ILE 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 71 ILE 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 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 97 HIS Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 60 CYS Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 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 92 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 80 GLN H 97 HIS H 175 ASN I 54 ASN I 97 HIS 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: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.095653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.074466 restraints weight = 31040.032| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.20 r_work: 0.2932 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17088 Z= 0.121 Angle : 0.495 6.366 23388 Z= 0.265 Chirality : 0.041 0.223 2796 Planarity : 0.003 0.022 2784 Dihedral : 3.246 13.193 2232 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.44 % Allowed : 20.54 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.08 (0.17), residues: 2028 helix: 3.17 (0.12), residues: 1404 sheet: 1.33 (0.48), residues: 132 loop : -1.36 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 32 TYR 0.008 0.001 TYR B 65 PHE 0.009 0.001 PHE K 180 TRP 0.005 0.001 TRP E 133 HIS 0.001 0.000 HIS I 73 Details of bonding type rmsd covalent geometry : bond 0.00278 (17052) covalent geometry : angle 0.49517 (23316) SS BOND : bond 0.00159 ( 36) SS BOND : angle 0.59314 ( 72) hydrogen bonds : bond 0.02791 ( 1224) hydrogen bonds : angle 3.11305 ( 3636) *********************** 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 357 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 293 time to evaluate : 0.701 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 66 ASP cc_start: 0.9113 (t70) cc_final: 0.8784 (t0) REVERT: A 211 TYR cc_start: 0.8560 (t80) cc_final: 0.8311 (t80) REVERT: A 215 ARG cc_start: 0.8676 (tpp-160) cc_final: 0.8123 (tpt170) REVERT: B 66 ASP cc_start: 0.9091 (t70) cc_final: 0.8631 (t0) REVERT: B 169 ASP cc_start: 0.8649 (p0) cc_final: 0.8438 (p0) REVERT: B 215 ARG cc_start: 0.8631 (tpp-160) cc_final: 0.8079 (tpt170) REVERT: C 20 ILE cc_start: 0.8571 (mp) cc_final: 0.8344 (mp) REVERT: C 46 ASP cc_start: 0.8836 (p0) cc_final: 0.8573 (p0) REVERT: C 133 TRP cc_start: 0.7393 (m-10) cc_final: 0.7070 (m-10) REVERT: C 203 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9095 (mp) REVERT: C 215 ARG cc_start: 0.8564 (tpp-160) cc_final: 0.8180 (tpt170) REVERT: D 66 ASP cc_start: 0.9098 (t70) cc_final: 0.8753 (t0) REVERT: D 169 ASP cc_start: 0.8677 (p0) cc_final: 0.8396 (p0) REVERT: D 211 TYR cc_start: 0.8583 (t80) cc_final: 0.8318 (t80) REVERT: D 215 ARG cc_start: 0.8657 (tpp-160) cc_final: 0.8156 (tpt170) REVERT: E 66 ASP cc_start: 0.9093 (t70) cc_final: 0.8631 (t0) REVERT: E 80 GLN cc_start: 0.9381 (tt0) cc_final: 0.9156 (tt0) REVERT: E 169 ASP cc_start: 0.8705 (p0) cc_final: 0.8495 (p0) REVERT: E 215 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8084 (tpt170) REVERT: F 93 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.9098 (mmt) REVERT: F 133 TRP cc_start: 0.7358 (m-10) cc_final: 0.7079 (m-10) REVERT: F 203 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9088 (mp) REVERT: F 215 ARG cc_start: 0.8580 (tpp-160) cc_final: 0.8199 (tpt170) REVERT: G 66 ASP cc_start: 0.9111 (t70) cc_final: 0.8767 (t0) REVERT: G 211 TYR cc_start: 0.8568 (t80) cc_final: 0.8311 (t80) REVERT: G 215 ARG cc_start: 0.8659 (tpp-160) cc_final: 0.8157 (tpt170) REVERT: H 66 ASP cc_start: 0.9108 (t70) cc_final: 0.8709 (t0) REVERT: H 93 MET cc_start: 0.9420 (tpp) cc_final: 0.9121 (mtp) REVERT: H 215 ARG cc_start: 0.8596 (tpp-160) cc_final: 0.8087 (tpt170) REVERT: I 20 ILE cc_start: 0.8575 (mp) cc_final: 0.8374 (mp) REVERT: I 133 TRP cc_start: 0.7370 (m-10) cc_final: 0.7095 (m-10) REVERT: I 215 ARG cc_start: 0.8577 (tpp-160) cc_final: 0.8172 (tpt170) REVERT: J 66 ASP cc_start: 0.9108 (t70) cc_final: 0.8765 (t0) REVERT: J 169 ASP cc_start: 0.8699 (p0) cc_final: 0.8434 (p0) REVERT: J 211 TYR cc_start: 0.8585 (t80) cc_final: 0.8311 (t80) REVERT: J 215 ARG cc_start: 0.8653 (tpp-160) cc_final: 0.8152 (tpt170) REVERT: K 66 ASP cc_start: 0.9099 (t70) cc_final: 0.8699 (t0) REVERT: K 93 MET cc_start: 0.9404 (tpp) cc_final: 0.9096 (mtp) REVERT: K 215 ARG cc_start: 0.8607 (tpp-160) cc_final: 0.8066 (tpt170) REVERT: L 20 ILE cc_start: 0.8581 (mp) cc_final: 0.8372 (mp) REVERT: L 133 TRP cc_start: 0.7397 (m100) cc_final: 0.7015 (m-10) REVERT: L 215 ARG cc_start: 0.8556 (tpp-160) cc_final: 0.8164 (tpt170) outliers start: 64 outliers final: 21 residues processed: 335 average time/residue: 0.6104 time to fit residues: 227.7804 Evaluate side-chains 304 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 280 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 134 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain F residue 60 CYS Chi-restraints excluded: chain F residue 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 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 97 HIS 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 106 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 97 HIS I 175 ASN J 54 ASN J 175 ASN K 80 GLN K 97 HIS K 175 ASN L 54 ASN L 175 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.074280 restraints weight = 31080.128| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.21 r_work: 0.2935 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17088 Z= 0.133 Angle : 0.511 7.062 23388 Z= 0.274 Chirality : 0.041 0.218 2796 Planarity : 0.003 0.023 2784 Dihedral : 3.255 13.346 2232 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.85 % Allowed : 21.13 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.10 (0.17), residues: 2028 helix: 3.16 (0.12), residues: 1404 sheet: 1.36 (0.48), residues: 132 loop : -1.31 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 32 TYR 0.008 0.001 TYR C 65 PHE 0.009 0.001 PHE K 180 TRP 0.005 0.001 TRP A 44 HIS 0.006 0.000 HIS L 97 Details of bonding type rmsd covalent geometry : bond 0.00309 (17052) covalent geometry : angle 0.51026 (23316) SS BOND : bond 0.00155 ( 36) SS BOND : angle 0.61632 ( 72) hydrogen bonds : bond 0.02802 ( 1224) hydrogen bonds : angle 3.10710 ( 3636) ********************** 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 336 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 283 time to evaluate : 0.724 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 66 ASP cc_start: 0.9121 (t70) cc_final: 0.8788 (t0) REVERT: A 211 TYR cc_start: 0.8548 (t80) cc_final: 0.8296 (t80) REVERT: A 215 ARG cc_start: 0.8702 (tpp-160) cc_final: 0.8125 (tpt170) REVERT: B 66 ASP cc_start: 0.9112 (t70) cc_final: 0.8651 (t0) REVERT: B 169 ASP cc_start: 0.8652 (p0) cc_final: 0.8444 (p0) REVERT: B 215 ARG cc_start: 0.8646 (tpp-160) cc_final: 0.8086 (tpt170) REVERT: C 20 ILE cc_start: 0.8559 (mp) cc_final: 0.8336 (mp) REVERT: C 46 ASP cc_start: 0.8855 (p0) cc_final: 0.8580 (p0) REVERT: C 133 TRP cc_start: 0.7384 (m-10) cc_final: 0.7060 (m-10) REVERT: C 203 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9069 (mp) REVERT: C 215 ARG cc_start: 0.8588 (tpp-160) cc_final: 0.8174 (tpt170) REVERT: D 66 ASP cc_start: 0.9114 (t70) cc_final: 0.8772 (t0) REVERT: D 169 ASP cc_start: 0.8668 (p0) cc_final: 0.8421 (p0) REVERT: D 211 TYR cc_start: 0.8558 (t80) cc_final: 0.8283 (t80) REVERT: D 215 ARG cc_start: 0.8689 (tpp-160) cc_final: 0.8161 (tpt170) REVERT: E 66 ASP cc_start: 0.9115 (t70) cc_final: 0.8650 (t0) REVERT: E 169 ASP cc_start: 0.8682 (p0) cc_final: 0.8471 (p0) REVERT: E 215 ARG cc_start: 0.8653 (tpp-160) cc_final: 0.8092 (tpt170) REVERT: F 93 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.9106 (mmt) REVERT: F 133 TRP cc_start: 0.7344 (m-10) cc_final: 0.7067 (m-10) REVERT: F 203 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9063 (mp) REVERT: F 215 ARG cc_start: 0.8613 (tpp-160) cc_final: 0.8195 (tpt170) REVERT: G 66 ASP cc_start: 0.9130 (t70) cc_final: 0.8782 (t0) REVERT: G 211 TYR cc_start: 0.8553 (t80) cc_final: 0.8290 (t80) REVERT: G 215 ARG cc_start: 0.8669 (tpp-160) cc_final: 0.8151 (tpt170) REVERT: H 66 ASP cc_start: 0.9121 (t70) cc_final: 0.8652 (t0) REVERT: H 93 MET cc_start: 0.9408 (tpp) cc_final: 0.9104 (mtp) REVERT: H 215 ARG cc_start: 0.8624 (tpp-160) cc_final: 0.8086 (tpt170) REVERT: I 20 ILE cc_start: 0.8573 (mp) cc_final: 0.8360 (mp) REVERT: I 133 TRP cc_start: 0.7363 (m-10) cc_final: 0.7096 (m-10) REVERT: I 215 ARG cc_start: 0.8600 (tpp-160) cc_final: 0.8162 (tpt170) REVERT: J 66 ASP cc_start: 0.9125 (t70) cc_final: 0.8780 (t0) REVERT: J 169 ASP cc_start: 0.8688 (p0) cc_final: 0.8441 (p0) REVERT: J 211 TYR cc_start: 0.8564 (t80) cc_final: 0.8283 (t80) REVERT: J 215 ARG cc_start: 0.8669 (tpp-160) cc_final: 0.8151 (tpt170) REVERT: K 66 ASP cc_start: 0.9110 (t70) cc_final: 0.8640 (t0) REVERT: K 93 MET cc_start: 0.9409 (tpp) cc_final: 0.9103 (mtp) REVERT: K 215 ARG cc_start: 0.8650 (tpp-160) cc_final: 0.8078 (tpt170) REVERT: L 20 ILE cc_start: 0.8572 (mp) cc_final: 0.8354 (mp) REVERT: L 133 TRP cc_start: 0.7391 (m100) cc_final: 0.7005 (m-10) REVERT: L 215 ARG cc_start: 0.8573 (tpp-160) cc_final: 0.8162 (tpt170) outliers start: 53 outliers final: 21 residues processed: 320 average time/residue: 0.5689 time to fit residues: 203.4315 Evaluate side-chains 303 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 279 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 134 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain F residue 60 CYS Chi-restraints excluded: chain F residue 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 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 80 GLN 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 128 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 195 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 175 ASN B 80 GLN B 97 HIS B 175 ASN C 54 ASN C 175 ASN D 54 ASN D 97 HIS 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 97 HIS I 175 ASN J 54 ASN J 175 ASN K 97 HIS K 175 ASN L 54 ASN L 94 HIS L 175 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.075014 restraints weight = 30989.240| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.21 r_work: 0.2951 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.2946 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= 0.122 Angle : 0.502 6.877 23388 Z= 0.269 Chirality : 0.040 0.189 2796 Planarity : 0.003 0.025 2784 Dihedral : 3.239 13.078 2232 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.28 % Allowed : 21.08 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.15 (0.17), residues: 2028 helix: 3.20 (0.12), residues: 1404 sheet: 1.41 (0.48), residues: 132 loop : -1.29 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 32 TYR 0.007 0.001 TYR L 65 PHE 0.009 0.001 PHE K 180 TRP 0.006 0.001 TRP J 44 HIS 0.007 0.000 HIS L 97 Details of bonding type rmsd covalent geometry : bond 0.00279 (17052) covalent geometry : angle 0.50150 (23316) SS BOND : bond 0.00143 ( 36) SS BOND : angle 0.58030 ( 72) hydrogen bonds : bond 0.02765 ( 1224) hydrogen bonds : angle 3.09161 ( 3636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5789.61 seconds wall clock time: 99 minutes 41.93 seconds (5981.93 seconds total)