Starting phenix.real_space_refine on Thu Mar 5 01:39:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z1t_14452/03_2026/7z1t_14452.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z1t_14452/03_2026/7z1t_14452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z1t_14452/03_2026/7z1t_14452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z1t_14452/03_2026/7z1t_14452.map" model { file = "/net/cci-nas-00/data/ceres_data/7z1t_14452/03_2026/7z1t_14452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z1t_14452/03_2026/7z1t_14452.cif" } resolution = 2.26 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 96 5.16 5 C 12396 2.51 5 N 2892 2.21 5 O 3108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18492 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 2.07, per 1000 atoms: 0.11 Number of scatterers: 18492 At special positions: 0 Unit cell: (100.062, 98.754, 158.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3108 8.00 N 2892 7.00 C 12396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 793.7 milliseconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 75.7% alpha, 3.7% 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 3 through 16 removed outlier: 4.090A pdb=" N LEU A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 105 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 152 through 177 Processing helix chain 'A' and resid 202 through 235 Processing helix chain 'B' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 105 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 152 through 177 Processing helix chain 'B' and resid 202 through 235 Processing helix chain 'C' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 105 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 152 through 177 Processing helix chain 'C' and resid 202 through 235 Processing helix chain 'D' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 105 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 152 through 177 Processing helix chain 'D' and resid 202 through 235 Processing helix chain 'E' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 45 removed outlier: 4.391A pdb=" N VAL E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU E 42 " --> pdb=" O GLY E 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 105 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 152 through 177 Processing helix chain 'E' and resid 202 through 235 Processing helix chain 'F' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU F 42 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER F 43 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 105 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 152 through 177 Processing helix chain 'F' and resid 202 through 235 Processing helix chain 'G' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU G 42 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER G 43 " --> pdb=" O THR G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 73 through 105 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 152 through 177 Processing helix chain 'G' and resid 202 through 235 Processing helix chain 'H' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU H 7 " --> pdb=" O ASP H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL H 41 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU H 42 " --> pdb=" O GLY H 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER H 43 " --> pdb=" O THR H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 73 through 105 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 152 through 177 Processing helix chain 'H' and resid 202 through 235 Processing helix chain 'I' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU I 7 " --> pdb=" O ASP I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU I 42 " --> pdb=" O GLY I 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER I 43 " --> pdb=" O THR I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 73 through 105 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 152 through 177 Processing helix chain 'I' and resid 202 through 235 Processing helix chain 'J' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU J 7 " --> pdb=" O ASP J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL J 41 " --> pdb=" O LEU J 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER J 43 " --> pdb=" O THR J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 73 through 105 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 152 through 177 Processing helix chain 'J' and resid 202 through 235 Processing helix chain 'K' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU K 7 " --> pdb=" O ASP K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL K 41 " --> pdb=" O LEU K 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU K 42 " --> pdb=" O GLY K 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER K 43 " --> pdb=" O THR K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 73 through 105 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 152 through 177 Processing helix chain 'K' and resid 202 through 235 Processing helix chain 'L' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU L 7 " --> pdb=" O ASP L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU L 42 " --> pdb=" O GLY L 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER L 43 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 73 through 105 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 152 through 177 Processing helix chain 'L' and resid 202 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 1416 hydrogen bonds defined for protein. 4176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5391 1.34 - 1.46: 4689 1.46 - 1.58: 8808 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 19008 Sorted by residual: bond pdb=" C ASP G 190 " pdb=" N PRO G 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.76e+00 bond pdb=" C ASP A 190 " pdb=" N PRO A 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.76e+00 bond pdb=" C ASP E 190 " pdb=" N PRO E 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.69e+00 bond pdb=" C ASP K 190 " pdb=" N PRO K 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.69e+00 bond pdb=" C ASP B 190 " pdb=" N PRO B 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.69e+00 ... (remaining 19003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 24699 1.16 - 2.32: 879 2.32 - 3.48: 132 3.48 - 4.64: 54 4.64 - 5.80: 36 Bond angle restraints: 25800 Sorted by residual: angle pdb=" C VAL C 87 " pdb=" CA VAL C 87 " pdb=" CB VAL C 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL I 87 " pdb=" CA VAL I 87 " pdb=" CB VAL I 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL F 87 " pdb=" CA VAL F 87 " pdb=" CB VAL F 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL L 87 " pdb=" CA VAL L 87 " pdb=" CB VAL L 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL B 87 " pdb=" CA VAL B 87 " pdb=" CB VAL B 87 " ideal model delta sigma weight residual 113.70 110.62 3.08 9.50e-01 1.11e+00 1.05e+01 ... (remaining 25795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 9828 17.21 - 34.42: 973 34.42 - 51.63: 227 51.63 - 68.83: 12 68.83 - 86.04: 24 Dihedral angle restraints: 11064 sinusoidal: 4392 harmonic: 6672 Sorted by residual: dihedral pdb=" CA TYR E 177 " pdb=" C TYR E 177 " pdb=" N GLY E 178 " pdb=" CA GLY E 178 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA TYR D 177 " pdb=" C TYR D 177 " pdb=" N GLY D 178 " pdb=" CA GLY D 178 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA TYR A 177 " pdb=" C TYR A 177 " pdb=" N GLY A 178 " pdb=" CA GLY A 178 " ideal model delta harmonic sigma weight residual 180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 11061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1976 0.027 - 0.054: 598 0.054 - 0.080: 275 0.080 - 0.107: 79 0.107 - 0.134: 24 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA ARG D 202 " pdb=" N ARG D 202 " pdb=" C ARG D 202 " pdb=" CB ARG D 202 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ARG H 202 " pdb=" N ARG H 202 " pdb=" C ARG H 202 " pdb=" CB ARG H 202 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ARG J 202 " pdb=" N ARG J 202 " pdb=" C ARG J 202 " pdb=" CB ARG J 202 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 2949 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU K 205 " 0.004 2.00e-02 2.50e+03 9.14e-03 8.36e-01 pdb=" CD GLU K 205 " -0.016 2.00e-02 2.50e+03 pdb=" OE1 GLU K 205 " 0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU K 205 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 205 " -0.004 2.00e-02 2.50e+03 9.12e-03 8.31e-01 pdb=" CD GLU H 205 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLU H 205 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU H 205 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 205 " -0.004 2.00e-02 2.50e+03 9.06e-03 8.20e-01 pdb=" CD GLU B 205 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLU B 205 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU B 205 " -0.006 2.00e-02 2.50e+03 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 238 2.71 - 3.26: 18591 3.26 - 3.81: 32196 3.81 - 4.35: 36542 4.35 - 4.90: 62100 Nonbonded interactions: 149667 Sorted by model distance: nonbonded pdb=" O ILE L 72 " pdb=" OH TYR L 177 " model vdw 2.163 3.040 nonbonded pdb=" O ILE I 72 " pdb=" OH TYR I 177 " model vdw 2.163 3.040 nonbonded pdb=" O ILE F 72 " pdb=" OH TYR F 177 " model vdw 2.163 3.040 nonbonded pdb=" O ILE C 72 " pdb=" OH TYR C 177 " model vdw 2.163 3.040 nonbonded pdb=" O ILE J 72 " pdb=" OH TYR J 177 " model vdw 2.164 3.040 ... (remaining 149662 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: 0.06 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: 6.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.650 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19044 Z= 0.136 Angle : 0.552 5.799 25872 Z= 0.307 Chirality : 0.034 0.134 2952 Planarity : 0.003 0.019 3096 Dihedral : 15.039 86.044 6636 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 3.21 (0.17), residues: 2220 helix: 3.20 (0.11), residues: 1680 sheet: -0.64 (0.35), residues: 204 loop : -2.06 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 53 TYR 0.010 0.002 TYR A 66 PHE 0.012 0.001 PHE K 32 TRP 0.004 0.001 TRP K 78 HIS 0.002 0.000 HIS G 74 Details of bonding type rmsd covalent geometry : bond 0.00275 (19008) covalent geometry : angle 0.55198 (25800) SS BOND : bond 0.00165 ( 36) SS BOND : angle 0.66397 ( 72) hydrogen bonds : bond 0.12909 ( 1416) hydrogen bonds : angle 3.50070 ( 4176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.762 Fit side-chains outliers start: 0 outliers final: 6 residues processed: 372 average time/residue: 0.7113 time to fit residues: 292.7196 Evaluate side-chains 329 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 323 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain L residue 12 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.102432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.072282 restraints weight = 28345.605| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.72 r_work: 0.2827 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 19044 Z= 0.126 Angle : 0.507 6.180 25872 Z= 0.259 Chirality : 0.036 0.116 2952 Planarity : 0.003 0.018 3096 Dihedral : 3.816 37.835 2448 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.73 % Allowed : 14.90 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 3.38 (0.17), residues: 2220 helix: 3.33 (0.11), residues: 1692 sheet: -0.42 (0.35), residues: 204 loop : -2.40 (0.25), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 76 TYR 0.019 0.001 TYR B 98 PHE 0.014 0.001 PHE F 32 TRP 0.006 0.001 TRP E 4 HIS 0.001 0.000 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00281 (19008) covalent geometry : angle 0.50622 (25800) SS BOND : bond 0.00226 ( 36) SS BOND : angle 0.73085 ( 72) hydrogen bonds : bond 0.04165 ( 1416) hydrogen bonds : angle 2.89616 ( 4176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 336 time to evaluate : 0.720 Fit side-chains REVERT: A 4 TRP cc_start: 0.7760 (OUTLIER) cc_final: 0.5982 (t-100) REVERT: A 202 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8928 (mtt-85) REVERT: B 202 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.8739 (ptp-170) REVERT: C 4 TRP cc_start: 0.7770 (OUTLIER) cc_final: 0.6680 (t-100) REVERT: D 4 TRP cc_start: 0.7757 (OUTLIER) cc_final: 0.5976 (t-100) REVERT: D 202 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8988 (mtt-85) REVERT: E 202 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8740 (ptp-170) REVERT: F 4 TRP cc_start: 0.7743 (OUTLIER) cc_final: 0.6662 (t-100) REVERT: G 4 TRP cc_start: 0.7755 (OUTLIER) cc_final: 0.5973 (t-100) REVERT: G 202 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8933 (mtt-85) REVERT: H 202 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8740 (ptp-170) REVERT: I 4 TRP cc_start: 0.7757 (OUTLIER) cc_final: 0.6679 (t-100) REVERT: J 4 TRP cc_start: 0.7756 (OUTLIER) cc_final: 0.5980 (t-100) REVERT: J 202 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8924 (mtt-85) REVERT: K 202 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8743 (ptp-170) REVERT: L 4 TRP cc_start: 0.7730 (OUTLIER) cc_final: 0.6645 (t-100) outliers start: 76 outliers final: 28 residues processed: 396 average time/residue: 0.7168 time to fit residues: 313.5557 Evaluate side-chains 348 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 304 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TRP Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 4 TRP Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 4 TRP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 4 TRP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 202 ARG Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 4 TRP Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 4 TRP Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 202 ARG Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 202 ARG Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 4 TRP Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 197 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.098626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.068626 restraints weight = 28760.511| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.73 r_work: 0.2757 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 19044 Z= 0.157 Angle : 0.514 6.121 25872 Z= 0.261 Chirality : 0.037 0.114 2952 Planarity : 0.003 0.021 3096 Dihedral : 3.509 19.089 2436 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.33 % Allowed : 16.08 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.39 (0.17), residues: 2220 helix: 3.32 (0.11), residues: 1692 sheet: -0.59 (0.36), residues: 204 loop : -2.18 (0.26), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 202 TYR 0.017 0.002 TYR B 98 PHE 0.014 0.002 PHE I 32 TRP 0.009 0.001 TRP C 4 HIS 0.002 0.001 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00374 (19008) covalent geometry : angle 0.51221 (25800) SS BOND : bond 0.00206 ( 36) SS BOND : angle 0.87082 ( 72) hydrogen bonds : bond 0.04302 ( 1416) hydrogen bonds : angle 2.96944 ( 4176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 318 time to evaluate : 0.750 Fit side-chains REVERT: A 202 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8684 (ptp-170) REVERT: B 202 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8799 (ptp-170) REVERT: D 202 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8957 (mtt-85) REVERT: E 202 ARG cc_start: 0.9290 (OUTLIER) cc_final: 0.8801 (ptp-170) REVERT: G 202 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8682 (ptp-170) REVERT: H 202 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.8796 (ptp-170) REVERT: J 202 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.8685 (ptp-170) REVERT: K 202 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.8797 (ptp-170) outliers start: 68 outliers final: 36 residues processed: 374 average time/residue: 0.7016 time to fit residues: 289.6563 Evaluate side-chains 348 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 304 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 202 ARG Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 202 ARG Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 202 ARG Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 183 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 158 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.101266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.071315 restraints weight = 28408.646| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.72 r_work: 0.2819 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 19044 Z= 0.100 Angle : 0.450 5.812 25872 Z= 0.226 Chirality : 0.034 0.101 2952 Planarity : 0.002 0.015 3096 Dihedral : 3.261 17.786 2436 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.94 % Allowed : 16.76 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 3.59 (0.17), residues: 2220 helix: 3.52 (0.11), residues: 1692 sheet: -0.76 (0.35), residues: 204 loop : -2.27 (0.27), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 101 TYR 0.015 0.001 TYR K 98 PHE 0.013 0.001 PHE A 32 TRP 0.005 0.001 TRP C 4 HIS 0.001 0.000 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00215 (19008) covalent geometry : angle 0.44940 (25800) SS BOND : bond 0.00177 ( 36) SS BOND : angle 0.65266 ( 72) hydrogen bonds : bond 0.03454 ( 1416) hydrogen bonds : angle 2.84487 ( 4176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 319 time to evaluate : 0.763 Fit side-chains REVERT: B 98 TYR cc_start: 0.8589 (m-80) cc_final: 0.8314 (m-80) REVERT: E 98 TYR cc_start: 0.8585 (m-80) cc_final: 0.8306 (m-80) REVERT: H 98 TYR cc_start: 0.8581 (m-80) cc_final: 0.8317 (m-80) outliers start: 60 outliers final: 28 residues processed: 363 average time/residue: 0.7332 time to fit residues: 293.2128 Evaluate side-chains 339 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 311 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 93 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.097972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.067947 restraints weight = 28421.338| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.70 r_work: 0.2751 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 19044 Z= 0.187 Angle : 0.515 6.680 25872 Z= 0.261 Chirality : 0.037 0.120 2952 Planarity : 0.003 0.018 3096 Dihedral : 3.472 18.997 2436 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.77 % Allowed : 15.88 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 3.48 (0.17), residues: 2220 helix: 3.39 (0.11), residues: 1692 sheet: -0.68 (0.37), residues: 204 loop : -2.11 (0.27), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 202 TYR 0.017 0.002 TYR K 98 PHE 0.025 0.002 PHE K 232 TRP 0.005 0.001 TRP L 4 HIS 0.002 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00453 (19008) covalent geometry : angle 0.51371 (25800) SS BOND : bond 0.00241 ( 36) SS BOND : angle 0.92354 ( 72) hydrogen bonds : bond 0.04242 ( 1416) hydrogen bonds : angle 2.98589 ( 4176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 319 time to evaluate : 0.744 Fit side-chains REVERT: B 98 TYR cc_start: 0.8631 (m-80) cc_final: 0.8333 (m-80) REVERT: B 152 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8933 (tp) REVERT: E 98 TYR cc_start: 0.8634 (m-80) cc_final: 0.8336 (m-80) REVERT: E 152 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8922 (tp) REVERT: F 13 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8631 (tptp) REVERT: H 98 TYR cc_start: 0.8649 (m-80) cc_final: 0.8366 (m-80) REVERT: H 152 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8923 (tp) REVERT: K 98 TYR cc_start: 0.8621 (m-80) cc_final: 0.8345 (m-80) REVERT: K 152 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8923 (tp) outliers start: 77 outliers final: 40 residues processed: 375 average time/residue: 0.6967 time to fit residues: 289.1000 Evaluate side-chains 354 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 309 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 163 optimal weight: 0.5980 chunk 57 optimal weight: 0.0980 chunk 139 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 199 optimal weight: 0.0030 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN C 49 GLN E 49 GLN H 49 GLN I 49 GLN K 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.101331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.071470 restraints weight = 28435.844| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.66 r_work: 0.2820 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 19044 Z= 0.093 Angle : 0.431 5.156 25872 Z= 0.216 Chirality : 0.033 0.100 2952 Planarity : 0.002 0.016 3096 Dihedral : 3.169 17.171 2436 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.16 % Allowed : 17.84 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 3.71 (0.17), residues: 2220 helix: 3.61 (0.11), residues: 1692 sheet: -0.71 (0.35), residues: 204 loop : -2.29 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 101 TYR 0.015 0.001 TYR H 98 PHE 0.025 0.001 PHE K 232 TRP 0.004 0.001 TRP F 4 HIS 0.001 0.000 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00191 (19008) covalent geometry : angle 0.42996 (25800) SS BOND : bond 0.00177 ( 36) SS BOND : angle 0.64029 ( 72) hydrogen bonds : bond 0.03116 ( 1416) hydrogen bonds : angle 2.81903 ( 4176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 326 time to evaluate : 0.817 Fit side-chains REVERT: B 98 TYR cc_start: 0.8627 (m-80) cc_final: 0.8339 (m-80) REVERT: B 152 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8828 (tp) REVERT: E 98 TYR cc_start: 0.8621 (m-80) cc_final: 0.8336 (m-80) REVERT: E 152 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8820 (tp) REVERT: H 98 TYR cc_start: 0.8630 (m-80) cc_final: 0.8308 (m-80) REVERT: H 152 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8808 (tp) REVERT: K 98 TYR cc_start: 0.8620 (m-80) cc_final: 0.8278 (m-80) REVERT: K 152 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8822 (tp) outliers start: 44 outliers final: 29 residues processed: 362 average time/residue: 0.6662 time to fit residues: 267.6865 Evaluate side-chains 349 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 316 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 140 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 190 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 199 optimal weight: 0.9980 chunk 209 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 GLN F 49 GLN K 49 GLN L 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.099329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.069520 restraints weight = 28558.244| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.71 r_work: 0.2776 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 19044 Z= 0.136 Angle : 0.464 6.131 25872 Z= 0.234 Chirality : 0.035 0.110 2952 Planarity : 0.003 0.016 3096 Dihedral : 3.290 17.960 2436 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.25 % Allowed : 17.65 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 3.66 (0.17), residues: 2220 helix: 3.55 (0.11), residues: 1692 sheet: -0.74 (0.36), residues: 204 loop : -2.13 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 101 TYR 0.015 0.001 TYR K 98 PHE 0.026 0.002 PHE E 232 TRP 0.004 0.001 TRP C 4 HIS 0.001 0.000 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00322 (19008) covalent geometry : angle 0.46329 (25800) SS BOND : bond 0.00207 ( 36) SS BOND : angle 0.77672 ( 72) hydrogen bonds : bond 0.03693 ( 1416) hydrogen bonds : angle 2.87634 ( 4176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 0.727 Fit side-chains REVERT: B 98 TYR cc_start: 0.8625 (m-80) cc_final: 0.8331 (m-80) REVERT: B 152 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8853 (tp) REVERT: E 98 TYR cc_start: 0.8617 (m-80) cc_final: 0.8328 (m-80) REVERT: E 152 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8858 (tp) REVERT: F 13 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8598 (tptp) REVERT: H 98 TYR cc_start: 0.8619 (m-80) cc_final: 0.8347 (m-80) REVERT: H 152 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8847 (tp) REVERT: I 13 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8630 (tptp) REVERT: K 98 TYR cc_start: 0.8625 (m-80) cc_final: 0.8343 (m-80) REVERT: K 152 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8853 (tp) outliers start: 46 outliers final: 34 residues processed: 349 average time/residue: 0.6988 time to fit residues: 268.7856 Evaluate side-chains 352 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 312 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 7 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 77 optimal weight: 0.0970 chunk 167 optimal weight: 2.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 GLN K 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.099161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.069037 restraints weight = 28328.832| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.66 r_work: 0.2764 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 19044 Z= 0.117 Angle : 0.460 5.840 25872 Z= 0.231 Chirality : 0.034 0.107 2952 Planarity : 0.003 0.018 3096 Dihedral : 3.254 17.671 2436 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.25 % Allowed : 17.65 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 3.67 (0.17), residues: 2220 helix: 3.55 (0.11), residues: 1692 sheet: -0.71 (0.35), residues: 204 loop : -2.13 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 101 TYR 0.015 0.001 TYR E 98 PHE 0.029 0.002 PHE H 232 TRP 0.004 0.001 TRP L 4 HIS 0.002 0.000 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00273 (19008) covalent geometry : angle 0.45864 (25800) SS BOND : bond 0.00200 ( 36) SS BOND : angle 0.75637 ( 72) hydrogen bonds : bond 0.03522 ( 1416) hydrogen bonds : angle 2.86332 ( 4176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 320 time to evaluate : 0.794 Fit side-chains REVERT: A 232 PHE cc_start: 0.7672 (t80) cc_final: 0.7144 (m-80) REVERT: B 98 TYR cc_start: 0.8603 (m-80) cc_final: 0.8294 (m-80) REVERT: B 152 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8818 (tp) REVERT: C 232 PHE cc_start: 0.7551 (t80) cc_final: 0.7064 (m-80) REVERT: D 232 PHE cc_start: 0.7679 (t80) cc_final: 0.7151 (m-80) REVERT: E 98 TYR cc_start: 0.8591 (m-80) cc_final: 0.8285 (m-80) REVERT: E 152 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8826 (tp) REVERT: F 13 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8564 (tptp) REVERT: F 232 PHE cc_start: 0.7543 (t80) cc_final: 0.7065 (m-80) REVERT: G 232 PHE cc_start: 0.7672 (t80) cc_final: 0.7140 (m-80) REVERT: H 98 TYR cc_start: 0.8599 (m-80) cc_final: 0.8302 (m-80) REVERT: H 152 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8816 (tp) REVERT: I 13 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8591 (tptp) REVERT: I 232 PHE cc_start: 0.7581 (t80) cc_final: 0.7142 (m-80) REVERT: J 232 PHE cc_start: 0.7671 (t80) cc_final: 0.7143 (m-80) REVERT: K 98 TYR cc_start: 0.8589 (m-80) cc_final: 0.8288 (m-80) REVERT: K 152 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8823 (tp) REVERT: L 232 PHE cc_start: 0.7542 (t80) cc_final: 0.7059 (m-80) outliers start: 46 outliers final: 34 residues processed: 353 average time/residue: 0.7174 time to fit residues: 279.6500 Evaluate side-chains 360 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 320 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 118 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 173 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.098516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.068473 restraints weight = 28616.340| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.68 r_work: 0.2757 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19044 Z= 0.129 Angle : 0.476 6.580 25872 Z= 0.238 Chirality : 0.034 0.109 2952 Planarity : 0.003 0.019 3096 Dihedral : 3.287 17.937 2436 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.96 % Allowed : 17.89 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 3.64 (0.17), residues: 2220 helix: 3.53 (0.11), residues: 1692 sheet: -0.72 (0.35), residues: 204 loop : -2.10 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 101 TYR 0.014 0.001 TYR K 98 PHE 0.029 0.002 PHE E 232 TRP 0.004 0.001 TRP F 4 HIS 0.002 0.000 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00308 (19008) covalent geometry : angle 0.47529 (25800) SS BOND : bond 0.00201 ( 36) SS BOND : angle 0.77414 ( 72) hydrogen bonds : bond 0.03641 ( 1416) hydrogen bonds : angle 2.87609 ( 4176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 312 time to evaluate : 0.741 Fit side-chains REVERT: A 232 PHE cc_start: 0.7723 (t80) cc_final: 0.7188 (m-80) REVERT: B 98 TYR cc_start: 0.8619 (m-80) cc_final: 0.8366 (m-80) REVERT: B 152 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8852 (tp) REVERT: C 232 PHE cc_start: 0.7576 (t80) cc_final: 0.7097 (m-80) REVERT: D 232 PHE cc_start: 0.7734 (t80) cc_final: 0.7198 (m-80) REVERT: E 98 TYR cc_start: 0.8626 (m-80) cc_final: 0.8375 (m-80) REVERT: E 152 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8855 (tp) REVERT: F 13 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8563 (tptp) REVERT: F 232 PHE cc_start: 0.7564 (t80) cc_final: 0.7109 (m-80) REVERT: G 232 PHE cc_start: 0.7722 (t80) cc_final: 0.7182 (m-80) REVERT: H 98 TYR cc_start: 0.8617 (m-80) cc_final: 0.8313 (m-80) REVERT: H 152 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8849 (tp) REVERT: I 13 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8570 (tptp) REVERT: I 232 PHE cc_start: 0.7577 (t80) cc_final: 0.7122 (m-80) REVERT: J 232 PHE cc_start: 0.7726 (t80) cc_final: 0.7191 (m-80) REVERT: K 98 TYR cc_start: 0.8629 (m-80) cc_final: 0.8329 (m-80) REVERT: K 152 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8858 (tp) REVERT: L 232 PHE cc_start: 0.7571 (t80) cc_final: 0.7110 (m-80) outliers start: 40 outliers final: 30 residues processed: 344 average time/residue: 0.7036 time to fit residues: 267.8380 Evaluate side-chains 344 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 308 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.100311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.070487 restraints weight = 28419.080| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.67 r_work: 0.2794 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19044 Z= 0.100 Angle : 0.452 5.725 25872 Z= 0.224 Chirality : 0.033 0.101 2952 Planarity : 0.002 0.018 3096 Dihedral : 3.162 16.821 2436 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.81 % Allowed : 17.94 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 3.68 (0.17), residues: 2220 helix: 3.57 (0.11), residues: 1692 sheet: -0.70 (0.35), residues: 204 loop : -2.17 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 101 TYR 0.013 0.001 TYR E 98 PHE 0.029 0.001 PHE H 232 TRP 0.004 0.001 TRP C 4 HIS 0.001 0.000 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00222 (19008) covalent geometry : angle 0.45139 (25800) SS BOND : bond 0.00166 ( 36) SS BOND : angle 0.67326 ( 72) hydrogen bonds : bond 0.03210 ( 1416) hydrogen bonds : angle 2.81371 ( 4176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 314 time to evaluate : 0.817 Fit side-chains REVERT: A 11 LEU cc_start: 0.8785 (tp) cc_final: 0.8527 (tm) REVERT: A 232 PHE cc_start: 0.7692 (t80) cc_final: 0.7130 (m-80) REVERT: B 98 TYR cc_start: 0.8606 (m-80) cc_final: 0.8375 (m-80) REVERT: C 232 PHE cc_start: 0.7518 (t80) cc_final: 0.6991 (m-80) REVERT: D 232 PHE cc_start: 0.7688 (t80) cc_final: 0.7127 (m-80) REVERT: E 98 TYR cc_start: 0.8606 (m-80) cc_final: 0.8363 (m-80) REVERT: F 13 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8551 (tptp) REVERT: F 232 PHE cc_start: 0.7513 (t80) cc_final: 0.6987 (m-80) REVERT: G 11 LEU cc_start: 0.8777 (tp) cc_final: 0.8517 (tm) REVERT: G 232 PHE cc_start: 0.7693 (t80) cc_final: 0.7129 (m-80) REVERT: H 98 TYR cc_start: 0.8603 (m-80) cc_final: 0.8374 (m-80) REVERT: I 232 PHE cc_start: 0.7512 (t80) cc_final: 0.7016 (m-80) REVERT: J 232 PHE cc_start: 0.7684 (t80) cc_final: 0.7122 (m-80) REVERT: K 98 TYR cc_start: 0.8599 (m-80) cc_final: 0.8369 (m-80) REVERT: L 232 PHE cc_start: 0.7518 (t80) cc_final: 0.6988 (m-80) outliers start: 37 outliers final: 31 residues processed: 346 average time/residue: 0.6806 time to fit residues: 261.1884 Evaluate side-chains 346 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 314 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 72 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 163 optimal weight: 0.0270 chunk 88 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 GLN K 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.097479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.067295 restraints weight = 28460.005| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.68 r_work: 0.2732 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 19044 Z= 0.168 Angle : 0.509 6.603 25872 Z= 0.257 Chirality : 0.036 0.116 2952 Planarity : 0.003 0.020 3096 Dihedral : 3.390 18.465 2436 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.62 % Allowed : 18.43 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 3.60 (0.17), residues: 2220 helix: 3.49 (0.11), residues: 1692 sheet: -0.73 (0.36), residues: 204 loop : -2.05 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 101 TYR 0.016 0.002 TYR E 98 PHE 0.029 0.002 PHE E 232 TRP 0.004 0.001 TRP C 4 HIS 0.002 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00407 (19008) covalent geometry : angle 0.50756 (25800) SS BOND : bond 0.00270 ( 36) SS BOND : angle 0.88445 ( 72) hydrogen bonds : bond 0.03970 ( 1416) hydrogen bonds : angle 2.93835 ( 4176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8044.46 seconds wall clock time: 137 minutes 19.76 seconds (8239.76 seconds total)