Starting phenix.real_space_refine on Mon Jun 16 02:43:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zxp_15013/06_2025/7zxp_15013.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zxp_15013/06_2025/7zxp_15013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zxp_15013/06_2025/7zxp_15013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zxp_15013/06_2025/7zxp_15013.map" model { file = "/net/cci-nas-00/data/ceres_data/7zxp_15013/06_2025/7zxp_15013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zxp_15013/06_2025/7zxp_15013.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 168 5.16 5 C 12192 2.51 5 N 3060 2.21 5 O 3000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18420 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1535 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 6.45, per 1000 atoms: 0.35 Number of scatterers: 18420 At special positions: 0 Unit cell: (106.602, 98.754, 164.154, 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 168 16.00 O 3000 8.00 N 3060 7.00 C 12192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 179 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 179 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 179 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 179 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 179 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 173 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 173 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 173 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 173 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 168 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 168 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 168 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 168 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 168 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.83 Conformation dependent library (CDL) restraints added in 2.3 seconds 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 74.9% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 107 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 220 Processing helix chain 'B' and resid 21 through 43 removed outlier: 3.735A pdb=" N GLU B 41 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 107 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 220 Processing helix chain 'C' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 107 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP C 133 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 134 " --> pdb=" O THR C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 220 Processing helix chain 'D' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 107 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 134 " --> pdb=" O THR D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 220 Processing helix chain 'E' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER E 42 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 107 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP E 133 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR E 134 " --> pdb=" O THR E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 220 Processing helix chain 'F' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU F 41 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER F 42 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 107 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP F 133 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR F 134 " --> pdb=" O THR F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 220 Processing helix chain 'G' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER G 42 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 107 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP G 133 " --> pdb=" O GLY G 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR G 134 " --> pdb=" O THR G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 220 Processing helix chain 'H' and resid 21 through 43 removed outlier: 3.735A pdb=" N GLU H 41 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 107 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP H 133 " --> pdb=" O GLY H 129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR H 134 " --> pdb=" O THR H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 220 Processing helix chain 'I' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER I 42 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 107 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP I 133 " --> pdb=" O GLY I 129 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR I 134 " --> pdb=" O THR I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 220 Processing helix chain 'J' and resid 21 through 43 removed outlier: 3.735A pdb=" N GLU J 41 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 107 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 123 through 157 removed outlier: 3.598A pdb=" N TRP J 133 " --> pdb=" O GLY J 129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR J 134 " --> pdb=" O THR J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 220 Processing helix chain 'K' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU K 41 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER K 42 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 107 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP K 133 " --> pdb=" O GLY K 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR K 134 " --> pdb=" O THR K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 220 Processing helix chain 'L' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU L 41 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER L 42 " --> pdb=" O VAL L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 107 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP L 133 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR L 134 " --> pdb=" O THR L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 220 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.841A 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: 3.841A 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: 3.841A 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: 3.841A 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: 3.841A 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: 3.841A 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: 3.841A 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: 3.841A 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: 3.841A 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: 3.841A 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: 3.841A 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: 3.841A pdb=" N ILE L 52 " --> pdb=" O PHE L 180 " (cutoff:3.500A) 1452 hydrogen bonds defined for protein. 4320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.96 Time building geometry restraints manager: 5.73 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: 5544 1.35 - 1.46: 4666 1.46 - 1.58: 8474 1.58 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 18924 Sorted by residual: bond pdb=" CA THR D 86 " pdb=" C THR D 86 " ideal model delta sigma weight residual 1.522 1.534 -0.013 1.26e-02 6.30e+03 9.91e-01 bond pdb=" CA THR G 86 " pdb=" C THR G 86 " ideal model delta sigma weight residual 1.522 1.534 -0.013 1.26e-02 6.30e+03 9.91e-01 bond pdb=" CA THR E 86 " pdb=" C THR E 86 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.26e-02 6.30e+03 9.82e-01 bond pdb=" CA THR K 86 " pdb=" C THR K 86 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.26e-02 6.30e+03 9.82e-01 bond pdb=" CA THR C 86 " pdb=" C THR C 86 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.26e-02 6.30e+03 9.58e-01 ... (remaining 18919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 25155 1.15 - 2.30: 501 2.30 - 3.46: 108 3.46 - 4.61: 0 4.61 - 5.76: 12 Bond angle restraints: 25776 Sorted by residual: angle pdb=" C THR K 86 " pdb=" N PRO K 87 " pdb=" CD PRO K 87 " ideal model delta sigma weight residual 125.00 130.76 -5.76 4.10e+00 5.95e-02 1.97e+00 angle pdb=" C THR I 86 " pdb=" N PRO I 87 " pdb=" CD PRO I 87 " ideal model delta sigma weight residual 125.00 130.75 -5.75 4.10e+00 5.95e-02 1.96e+00 angle pdb=" C THR L 86 " pdb=" N PRO L 87 " pdb=" CD PRO L 87 " ideal model delta sigma weight residual 125.00 130.75 -5.75 4.10e+00 5.95e-02 1.96e+00 angle pdb=" C THR H 86 " pdb=" N PRO H 87 " pdb=" CD PRO H 87 " ideal model delta sigma weight residual 125.00 130.72 -5.72 4.10e+00 5.95e-02 1.95e+00 angle pdb=" C THR B 86 " pdb=" N PRO B 87 " pdb=" CD PRO B 87 " ideal model delta sigma weight residual 125.00 130.71 -5.71 4.10e+00 5.95e-02 1.94e+00 ... (remaining 25771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.86: 9372 12.86 - 25.72: 1032 25.72 - 38.58: 420 38.58 - 51.44: 240 51.44 - 64.30: 36 Dihedral angle restraints: 11100 sinusoidal: 4320 harmonic: 6780 Sorted by residual: dihedral pdb=" CB CYS J 64 " pdb=" SG CYS J 64 " pdb=" SG CYS J 168 " pdb=" CB CYS J 168 " ideal model delta sinusoidal sigma weight residual -86.00 -117.20 31.20 1 1.00e+01 1.00e-02 1.39e+01 dihedral pdb=" CB CYS D 64 " pdb=" SG CYS D 64 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual -86.00 -117.20 31.20 1 1.00e+01 1.00e-02 1.39e+01 dihedral pdb=" CB CYS E 64 " pdb=" SG CYS E 64 " pdb=" SG CYS E 168 " pdb=" CB CYS E 168 " ideal model delta sinusoidal sigma weight residual -86.00 -117.19 31.19 1 1.00e+01 1.00e-02 1.39e+01 ... (remaining 11097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2182 0.033 - 0.067: 590 0.067 - 0.100: 228 0.100 - 0.134: 12 0.134 - 0.167: 36 Chirality restraints: 3048 Sorted by residual: chirality pdb=" CB VAL C 95 " pdb=" CA VAL C 95 " pdb=" CG1 VAL C 95 " pdb=" CG2 VAL C 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CB VAL F 95 " pdb=" CA VAL F 95 " pdb=" CG1 VAL F 95 " pdb=" CG2 VAL F 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CB VAL L 95 " pdb=" CA VAL L 95 " pdb=" CG1 VAL L 95 " pdb=" CG2 VAL L 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 3045 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 29 " -0.013 2.00e-02 2.50e+03 1.28e-02 2.88e+00 pdb=" CG PHE H 29 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE H 29 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE H 29 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE H 29 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE H 29 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE H 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 29 " -0.013 2.00e-02 2.50e+03 1.28e-02 2.87e+00 pdb=" CG PHE K 29 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE K 29 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE K 29 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE K 29 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE K 29 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE K 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 29 " -0.013 2.00e-02 2.50e+03 1.28e-02 2.86e+00 pdb=" CG PHE J 29 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE J 29 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE J 29 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE J 29 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE J 29 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE J 29 " 0.000 2.00e-02 2.50e+03 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 6007 2.85 - 3.36: 18839 3.36 - 3.87: 32223 3.87 - 4.39: 32415 4.39 - 4.90: 58673 Nonbonded interactions: 148157 Sorted by model distance: nonbonded pdb=" O LEU D 131 " pdb=" OG1 THR D 134 " model vdw 2.332 3.040 nonbonded pdb=" O LEU I 131 " pdb=" OG1 THR I 134 " model vdw 2.332 3.040 nonbonded pdb=" O LEU L 131 " pdb=" OG1 THR L 134 " model vdw 2.332 3.040 nonbonded pdb=" O LEU F 131 " pdb=" OG1 THR F 134 " model vdw 2.332 3.040 nonbonded pdb=" O LEU C 131 " pdb=" OG1 THR C 134 " model vdw 2.332 3.040 ... (remaining 148152 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 73.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 38.070 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:34.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 0.020 18960 Z= 0.114 Angle : 0.423 5.761 25848 Z= 0.242 Chirality : 0.039 0.167 3048 Planarity : 0.003 0.017 3084 Dihedral : 14.726 64.301 6576 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.17 % Allowed : 17.35 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.20 (0.17), residues: 2244 helix: 4.00 (0.10), residues: 1632 sheet: -0.27 (0.43), residues: 204 loop : -1.17 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 132 HIS 0.003 0.001 HIS H 73 PHE 0.030 0.002 PHE H 29 TYR 0.008 0.001 TYR G 65 ARG 0.002 0.000 ARG I 75 Details of bonding type rmsd hydrogen bonds : bond 0.08696 ( 1452) hydrogen bonds : angle 3.55967 ( 4320) SS BOND : bond 0.00063 ( 36) SS BOND : angle 0.58879 ( 72) covalent geometry : bond 0.00197 (18924) covalent geometry : angle 0.42292 (25776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 290 time to evaluate : 1.892 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 314 average time/residue: 1.0928 time to fit residues: 402.8875 Evaluate side-chains 207 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain L residue 42 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 178 optimal weight: 10.0000 chunk 69 optimal weight: 0.4980 chunk 108 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS D 73 HIS G 73 HIS H 73 HIS J 73 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.134602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.083712 restraints weight = 25483.730| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.90 r_work: 0.2938 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 18960 Z= 0.120 Angle : 0.428 5.614 25848 Z= 0.230 Chirality : 0.039 0.163 3048 Planarity : 0.003 0.016 3084 Dihedral : 3.857 39.779 2504 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.27 % Allowed : 17.01 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.42 (0.16), residues: 2244 helix: 4.16 (0.10), residues: 1632 sheet: -0.32 (0.42), residues: 204 loop : -0.99 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 133 HIS 0.005 0.001 HIS F 73 PHE 0.010 0.002 PHE D 68 TYR 0.012 0.001 TYR D 65 ARG 0.001 0.000 ARG L 32 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 1452) hydrogen bonds : angle 3.05064 ( 4320) SS BOND : bond 0.00142 ( 36) SS BOND : angle 0.95083 ( 72) covalent geometry : bond 0.00269 (18924) covalent geometry : angle 0.42547 (25776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 214 time to evaluate : 1.813 Fit side-chains REVERT: A 105 MET cc_start: 0.3186 (OUTLIER) cc_final: 0.2934 (tpp) REVERT: B 105 MET cc_start: 0.3238 (OUTLIER) cc_final: 0.3009 (tpp) REVERT: D 105 MET cc_start: 0.3181 (OUTLIER) cc_final: 0.2934 (tpp) REVERT: E 105 MET cc_start: 0.3227 (OUTLIER) cc_final: 0.2991 (tpt) REVERT: G 105 MET cc_start: 0.3185 (OUTLIER) cc_final: 0.2936 (tpp) REVERT: H 105 MET cc_start: 0.3218 (OUTLIER) cc_final: 0.2997 (tpp) REVERT: J 105 MET cc_start: 0.3192 (OUTLIER) cc_final: 0.2941 (tpp) REVERT: K 105 MET cc_start: 0.3227 (OUTLIER) cc_final: 0.3000 (tpp) outliers start: 67 outliers final: 12 residues processed: 251 average time/residue: 1.3109 time to fit residues: 375.2832 Evaluate side-chains 201 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 44 optimal weight: 0.8980 chunk 133 optimal weight: 20.0000 chunk 175 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.134428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.083751 restraints weight = 25416.548| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.88 r_work: 0.2947 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 18960 Z= 0.108 Angle : 0.410 5.626 25848 Z= 0.218 Chirality : 0.038 0.163 3048 Planarity : 0.002 0.014 3084 Dihedral : 3.706 40.713 2492 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.19 % Allowed : 16.57 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.56 (0.16), residues: 2244 helix: 4.28 (0.10), residues: 1632 sheet: -0.29 (0.42), residues: 204 loop : -1.03 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 133 HIS 0.004 0.001 HIS C 73 PHE 0.009 0.002 PHE A 180 TYR 0.012 0.001 TYR K 65 ARG 0.002 0.000 ARG J 32 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 1452) hydrogen bonds : angle 2.94248 ( 4320) SS BOND : bond 0.00126 ( 36) SS BOND : angle 0.77327 ( 72) covalent geometry : bond 0.00240 (18924) covalent geometry : angle 0.40882 (25776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 182 time to evaluate : 2.335 Fit side-chains REVERT: A 105 MET cc_start: 0.3170 (OUTLIER) cc_final: 0.2927 (tpp) REVERT: D 105 MET cc_start: 0.3166 (OUTLIER) cc_final: 0.2924 (tpp) REVERT: G 105 MET cc_start: 0.3169 (OUTLIER) cc_final: 0.2924 (tpp) REVERT: J 105 MET cc_start: 0.3157 (OUTLIER) cc_final: 0.2915 (tpp) outliers start: 86 outliers final: 44 residues processed: 248 average time/residue: 1.0152 time to fit residues: 290.8826 Evaluate side-chains 224 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 97 HIS Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 225 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 161 optimal weight: 30.0000 chunk 145 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 9 optimal weight: 40.0000 chunk 164 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 HIS F 73 HIS I 73 HIS L 73 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.131183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.080115 restraints weight = 25346.428| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.85 r_work: 0.2868 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 18960 Z= 0.177 Angle : 0.470 5.842 25848 Z= 0.254 Chirality : 0.041 0.174 3048 Planarity : 0.003 0.019 3084 Dihedral : 3.997 42.520 2492 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 3.90 % Allowed : 17.11 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.39 (0.16), residues: 2244 helix: 4.12 (0.10), residues: 1632 sheet: -0.25 (0.42), residues: 204 loop : -0.98 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 133 HIS 0.005 0.001 HIS I 73 PHE 0.015 0.002 PHE E 180 TYR 0.015 0.001 TYR H 65 ARG 0.003 0.000 ARG J 32 Details of bonding type rmsd hydrogen bonds : bond 0.04491 ( 1452) hydrogen bonds : angle 3.08704 ( 4320) SS BOND : bond 0.00164 ( 36) SS BOND : angle 1.14719 ( 72) covalent geometry : bond 0.00425 (18924) covalent geometry : angle 0.46692 (25776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 177 time to evaluate : 1.919 Fit side-chains REVERT: A 105 MET cc_start: 0.3147 (OUTLIER) cc_final: 0.2909 (tpp) REVERT: B 105 MET cc_start: 0.3279 (OUTLIER) cc_final: 0.3041 (tpp) REVERT: C 105 MET cc_start: 0.3065 (OUTLIER) cc_final: 0.2735 (tpp) REVERT: D 105 MET cc_start: 0.3156 (OUTLIER) cc_final: 0.2917 (tpp) REVERT: E 105 MET cc_start: 0.3229 (OUTLIER) cc_final: 0.2996 (tpp) REVERT: F 105 MET cc_start: 0.3045 (OUTLIER) cc_final: 0.2710 (tpp) REVERT: G 105 MET cc_start: 0.3145 (OUTLIER) cc_final: 0.2909 (tpp) REVERT: H 105 MET cc_start: 0.3267 (OUTLIER) cc_final: 0.3033 (tpp) REVERT: I 105 MET cc_start: 0.3072 (OUTLIER) cc_final: 0.2737 (tpp) REVERT: J 105 MET cc_start: 0.3151 (OUTLIER) cc_final: 0.2911 (tpp) REVERT: K 105 MET cc_start: 0.3271 (OUTLIER) cc_final: 0.3040 (tpp) REVERT: L 105 MET cc_start: 0.3028 (OUTLIER) cc_final: 0.2704 (tpp) outliers start: 80 outliers final: 32 residues processed: 207 average time/residue: 1.0268 time to fit residues: 245.2233 Evaluate side-chains 215 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 97 HIS Chi-restraints excluded: chain L residue 105 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 75 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 47 optimal weight: 30.0000 chunk 24 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 170 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.131032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080660 restraints weight = 25355.620| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.83 r_work: 0.2876 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 18960 Z= 0.163 Angle : 0.448 5.684 25848 Z= 0.241 Chirality : 0.040 0.170 3048 Planarity : 0.003 0.020 3084 Dihedral : 3.928 41.848 2492 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.36 % Allowed : 17.54 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.34 (0.17), residues: 2244 helix: 4.10 (0.10), residues: 1632 sheet: -0.26 (0.42), residues: 204 loop : -1.06 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 133 HIS 0.004 0.001 HIS B 73 PHE 0.014 0.002 PHE A 180 TYR 0.015 0.001 TYR D 65 ARG 0.002 0.000 ARG D 32 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 1452) hydrogen bonds : angle 3.05710 ( 4320) SS BOND : bond 0.00177 ( 36) SS BOND : angle 1.05592 ( 72) covalent geometry : bond 0.00392 (18924) covalent geometry : angle 0.44498 (25776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 172 time to evaluate : 2.062 Fit side-chains REVERT: B 105 MET cc_start: 0.3388 (OUTLIER) cc_final: 0.3043 (tpp) REVERT: C 105 MET cc_start: 0.3256 (OUTLIER) cc_final: 0.2847 (tpp) REVERT: E 105 MET cc_start: 0.3419 (OUTLIER) cc_final: 0.3074 (tpp) REVERT: F 105 MET cc_start: 0.3260 (OUTLIER) cc_final: 0.2843 (tpp) REVERT: H 105 MET cc_start: 0.3413 (OUTLIER) cc_final: 0.3075 (tpp) REVERT: I 105 MET cc_start: 0.3249 (OUTLIER) cc_final: 0.2838 (tpp) REVERT: K 105 MET cc_start: 0.3378 (OUTLIER) cc_final: 0.3034 (tpp) REVERT: L 105 MET cc_start: 0.3259 (OUTLIER) cc_final: 0.2852 (tpp) outliers start: 69 outliers final: 32 residues processed: 205 average time/residue: 1.0643 time to fit residues: 251.0629 Evaluate side-chains 210 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 105 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 186 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 203 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.132357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.082240 restraints weight = 25456.271| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.85 r_work: 0.2902 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 18960 Z= 0.108 Angle : 0.403 5.688 25848 Z= 0.216 Chirality : 0.038 0.166 3048 Planarity : 0.002 0.017 3084 Dihedral : 3.727 40.985 2492 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.31 % Allowed : 17.54 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.58 (0.17), residues: 2244 helix: 4.29 (0.10), residues: 1632 sheet: -0.14 (0.43), residues: 204 loop : -1.08 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 133 HIS 0.003 0.001 HIS B 73 PHE 0.009 0.002 PHE J 180 TYR 0.017 0.001 TYR C 211 ARG 0.002 0.000 ARG J 32 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 1452) hydrogen bonds : angle 2.89155 ( 4320) SS BOND : bond 0.00113 ( 36) SS BOND : angle 0.81947 ( 72) covalent geometry : bond 0.00241 (18924) covalent geometry : angle 0.40090 (25776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 208 time to evaluate : 1.947 Fit side-chains outliers start: 68 outliers final: 32 residues processed: 232 average time/residue: 0.9219 time to fit residues: 251.2776 Evaluate side-chains 232 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 146 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 148 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 204 optimal weight: 0.4980 chunk 167 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS E 97 HIS G 97 HIS H 97 HIS J 97 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.130809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.079386 restraints weight = 25402.714| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.90 r_work: 0.2839 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 18960 Z= 0.104 Angle : 0.393 6.195 25848 Z= 0.213 Chirality : 0.038 0.208 3048 Planarity : 0.002 0.017 3084 Dihedral : 3.674 40.909 2492 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.88 % Allowed : 17.98 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.74 (0.16), residues: 2244 helix: 4.42 (0.10), residues: 1632 sheet: -0.10 (0.44), residues: 204 loop : -1.10 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 132 HIS 0.003 0.000 HIS K 73 PHE 0.009 0.002 PHE J 180 TYR 0.014 0.001 TYR C 211 ARG 0.002 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 1452) hydrogen bonds : angle 2.80005 ( 4320) SS BOND : bond 0.00108 ( 36) SS BOND : angle 0.79032 ( 72) covalent geometry : bond 0.00228 (18924) covalent geometry : angle 0.39151 (25776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 197 time to evaluate : 1.892 Fit side-chains outliers start: 59 outliers final: 35 residues processed: 225 average time/residue: 0.9444 time to fit residues: 248.2267 Evaluate side-chains 224 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 67 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 215 optimal weight: 0.5980 chunk 189 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 97 HIS B 97 HIS C 97 HIS E 97 HIS G 97 HIS H 97 HIS J 97 HIS K 97 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.131543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.080342 restraints weight = 25516.510| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.89 r_work: 0.2861 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 18960 Z= 0.095 Angle : 0.383 6.478 25848 Z= 0.207 Chirality : 0.038 0.179 3048 Planarity : 0.002 0.015 3084 Dihedral : 3.599 40.416 2492 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.58 % Allowed : 18.42 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.85 (0.16), residues: 2244 helix: 4.52 (0.09), residues: 1632 sheet: -0.06 (0.44), residues: 204 loop : -1.13 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP J 132 HIS 0.003 0.000 HIS K 73 PHE 0.007 0.001 PHE L 190 TYR 0.014 0.001 TYR G 211 ARG 0.002 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 1452) hydrogen bonds : angle 2.73119 ( 4320) SS BOND : bond 0.00100 ( 36) SS BOND : angle 0.72546 ( 72) covalent geometry : bond 0.00199 (18924) covalent geometry : angle 0.38191 (25776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 2.048 Fit side-chains outliers start: 53 outliers final: 32 residues processed: 228 average time/residue: 0.9888 time to fit residues: 262.0897 Evaluate side-chains 236 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 143 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 199 optimal weight: 40.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS C 97 HIS E 97 HIS F 97 HIS G 97 HIS H 97 HIS I 97 HIS J 97 HIS K 97 HIS L 97 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.128984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.077039 restraints weight = 25741.627| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.89 r_work: 0.2792 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18960 Z= 0.149 Angle : 0.438 6.665 25848 Z= 0.239 Chirality : 0.040 0.204 3048 Planarity : 0.003 0.016 3084 Dihedral : 3.844 41.899 2492 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.78 % Allowed : 19.01 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.60 (0.16), residues: 2244 helix: 4.32 (0.10), residues: 1632 sheet: -0.14 (0.43), residues: 204 loop : -1.14 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 44 HIS 0.004 0.001 HIS B 73 PHE 0.012 0.002 PHE J 180 TYR 0.019 0.002 TYR L 211 ARG 0.002 0.000 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 1452) hydrogen bonds : angle 2.87145 ( 4320) SS BOND : bond 0.00121 ( 36) SS BOND : angle 0.97347 ( 72) covalent geometry : bond 0.00355 (18924) covalent geometry : angle 0.43522 (25776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 188 time to evaluate : 2.095 Fit side-chains outliers start: 57 outliers final: 32 residues processed: 223 average time/residue: 0.9380 time to fit residues: 244.2628 Evaluate side-chains 211 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 218 optimal weight: 30.0000 chunk 211 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS C 97 HIS E 97 HIS G 97 HIS H 97 HIS K 97 HIS L 97 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.127369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.075413 restraints weight = 25544.564| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.86 r_work: 0.2755 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 18960 Z= 0.214 Angle : 0.488 6.513 25848 Z= 0.268 Chirality : 0.042 0.195 3048 Planarity : 0.003 0.022 3084 Dihedral : 4.085 43.211 2492 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.34 % Allowed : 19.74 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.22 (0.16), residues: 2244 helix: 4.00 (0.10), residues: 1632 sheet: -0.28 (0.42), residues: 204 loop : -1.07 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 77 HIS 0.005 0.001 HIS K 73 PHE 0.016 0.003 PHE E 180 TYR 0.020 0.002 TYR A 211 ARG 0.002 0.000 ARG D 32 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 1452) hydrogen bonds : angle 3.07561 ( 4320) SS BOND : bond 0.00217 ( 36) SS BOND : angle 1.21729 ( 72) covalent geometry : bond 0.00525 (18924) covalent geometry : angle 0.48478 (25776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 2.220 Fit side-chains REVERT: C 93 MET cc_start: 0.8749 (mtt) cc_final: 0.8498 (mtt) REVERT: L 93 MET cc_start: 0.8752 (mtt) cc_final: 0.8505 (mtt) outliers start: 48 outliers final: 32 residues processed: 250 average time/residue: 1.1077 time to fit residues: 317.3360 Evaluate side-chains 230 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 164 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.130614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.079501 restraints weight = 25590.322| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.89 r_work: 0.2846 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18960 Z= 0.098 Angle : 0.394 6.506 25848 Z= 0.214 Chirality : 0.038 0.181 3048 Planarity : 0.002 0.016 3084 Dihedral : 3.659 41.009 2492 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.27 % Allowed : 21.54 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.77 (0.17), residues: 2244 helix: 4.46 (0.10), residues: 1632 sheet: -0.10 (0.44), residues: 204 loop : -1.16 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 132 HIS 0.003 0.000 HIS B 73 PHE 0.007 0.001 PHE J 180 TYR 0.014 0.001 TYR H 211 ARG 0.002 0.000 ARG J 32 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 1452) hydrogen bonds : angle 2.80391 ( 4320) SS BOND : bond 0.00110 ( 36) SS BOND : angle 0.73125 ( 72) covalent geometry : bond 0.00207 (18924) covalent geometry : angle 0.39228 (25776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16412.64 seconds wall clock time: 280 minutes 23.59 seconds (16823.59 seconds total)