Starting phenix.real_space_refine on Thu Nov 20 07:32:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mhq_9116/11_2025/6mhq_9116.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mhq_9116/11_2025/6mhq_9116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6mhq_9116/11_2025/6mhq_9116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mhq_9116/11_2025/6mhq_9116.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mhq_9116/11_2025/6mhq_9116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mhq_9116/11_2025/6mhq_9116.map" } resolution = 3.4 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= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 11568 2.51 5 N 2772 2.21 5 O 2940 1.98 5 H 15264 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32640 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2720 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 3.42, per 1000 atoms: 0.10 Number of scatterers: 32640 At special positions: 0 Unit cell: (95.095, 92.435, 134.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 O 2940 8.00 N 2772 7.00 C 11568 6.00 H 15264 1.00 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 189 " distance=2.02 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 189 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 189 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 189 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 189 " distance=2.02 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 189 " distance=2.02 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 189 " distance=2.02 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 189 " distance=2.02 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 189 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 189 " distance=2.02 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 189 " distance=2.02 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 183 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 183 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 183 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 183 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 183 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 183 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 183 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 178 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 178 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 178 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 178 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 178 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 178 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 178 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 178 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 178 " 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: 2.87 Conformation dependent library (CDL) restraints added in 880.5 milliseconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4008 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 77.4% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 removed outlier: 3.879A pdb=" N GLU A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 32 through 40 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 97 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 143 through 168 Processing helix chain 'A' and resid 193 through 222 removed outlier: 3.763A pdb=" N TYR A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 16 removed outlier: 3.878A pdb=" N GLU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 32 Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 97 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 143 through 168 Processing helix chain 'B' and resid 193 through 222 removed outlier: 3.763A pdb=" N TYR B 220 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 16 removed outlier: 3.878A pdb=" N GLU C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 32 Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 97 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 143 through 168 Processing helix chain 'C' and resid 193 through 222 removed outlier: 3.763A pdb=" N TYR C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 16 removed outlier: 3.879A pdb=" N GLU D 16 " --> pdb=" O GLU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 32 Processing helix chain 'D' and resid 32 through 40 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 97 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 143 through 168 Processing helix chain 'D' and resid 193 through 222 removed outlier: 3.764A pdb=" N TYR D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 16 removed outlier: 3.878A pdb=" N GLU E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 32 through 40 Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 97 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 143 through 168 Processing helix chain 'E' and resid 193 through 222 removed outlier: 3.763A pdb=" N TYR E 220 " --> pdb=" O VAL E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 16 removed outlier: 3.879A pdb=" N GLU F 16 " --> pdb=" O GLU F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 32 Processing helix chain 'F' and resid 32 through 40 Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 97 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 143 through 168 Processing helix chain 'F' and resid 193 through 222 removed outlier: 3.763A pdb=" N TYR F 220 " --> pdb=" O VAL F 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 16 removed outlier: 3.879A pdb=" N GLU G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 32 Processing helix chain 'G' and resid 32 through 40 Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 73 through 97 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 143 through 168 Processing helix chain 'G' and resid 193 through 222 removed outlier: 3.763A pdb=" N TYR G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 16 removed outlier: 3.879A pdb=" N GLU H 16 " --> pdb=" O GLU H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 32 Processing helix chain 'H' and resid 32 through 40 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 73 through 97 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 143 through 168 Processing helix chain 'H' and resid 193 through 222 removed outlier: 3.764A pdb=" N TYR H 220 " --> pdb=" O VAL H 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 16 removed outlier: 3.879A pdb=" N GLU I 16 " --> pdb=" O GLU I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 32 Processing helix chain 'I' and resid 32 through 40 Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 46 through 48 No H-bonds generated for 'chain 'I' and resid 46 through 48' Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 73 through 97 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 143 through 168 Processing helix chain 'I' and resid 193 through 222 removed outlier: 3.764A pdb=" N TYR I 220 " --> pdb=" O VAL I 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 16 removed outlier: 3.879A pdb=" N GLU J 16 " --> pdb=" O GLU J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 32 Processing helix chain 'J' and resid 32 through 40 Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 46 through 48 No H-bonds generated for 'chain 'J' and resid 46 through 48' Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 73 through 97 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 143 through 168 Processing helix chain 'J' and resid 193 through 222 removed outlier: 3.764A pdb=" N TYR J 220 " --> pdb=" O VAL J 216 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 16 removed outlier: 3.877A pdb=" N GLU K 16 " --> pdb=" O GLU K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 32 Processing helix chain 'K' and resid 32 through 40 Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 46 through 48 No H-bonds generated for 'chain 'K' and resid 46 through 48' Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 73 through 97 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 143 through 168 Processing helix chain 'K' and resid 193 through 222 removed outlier: 3.763A pdb=" N TYR K 220 " --> pdb=" O VAL K 216 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 16 removed outlier: 3.878A pdb=" N GLU L 16 " --> pdb=" O GLU L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 32 Processing helix chain 'L' and resid 32 through 40 Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 46 through 48 No H-bonds generated for 'chain 'L' and resid 46 through 48' Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 73 through 97 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 143 through 168 Processing helix chain 'L' and resid 193 through 222 removed outlier: 3.764A pdb=" N TYR L 220 " --> pdb=" O VAL L 216 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 178 Processing sheet with id=AA2, first strand: chain 'B' and resid 175 through 178 Processing sheet with id=AA3, first strand: chain 'C' and resid 175 through 178 Processing sheet with id=AA4, first strand: chain 'D' and resid 175 through 178 Processing sheet with id=AA5, first strand: chain 'E' and resid 175 through 178 Processing sheet with id=AA6, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AA7, first strand: chain 'G' and resid 175 through 178 Processing sheet with id=AA8, first strand: chain 'H' and resid 175 through 178 Processing sheet with id=AA9, first strand: chain 'I' and resid 175 through 178 Processing sheet with id=AB1, first strand: chain 'J' and resid 175 through 178 Processing sheet with id=AB2, first strand: chain 'K' and resid 175 through 178 Processing sheet with id=AB3, first strand: chain 'L' and resid 175 through 178 1212 hydrogen bonds defined for protein. 3600 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: 7.69 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 15252 1.02 - 1.22: 12 1.22 - 1.41: 7824 1.41 - 1.61: 9948 1.61 - 1.80: 108 Bond restraints: 33144 Sorted by residual: bond pdb=" CB VAL G 187 " pdb=" CG1 VAL G 187 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.77e+00 bond pdb=" CB VAL A 187 " pdb=" CG1 VAL A 187 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.77e+00 bond pdb=" CB VAL B 187 " pdb=" CG1 VAL B 187 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.76e+00 bond pdb=" CB VAL H 187 " pdb=" CG1 VAL H 187 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.71e+00 bond pdb=" CB VAL L 187 " pdb=" CG1 VAL L 187 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.70e+00 ... (remaining 33139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 51276 1.27 - 2.55: 7063 2.55 - 3.82: 654 3.82 - 5.09: 131 5.09 - 6.36: 84 Bond angle restraints: 59208 Sorted by residual: angle pdb=" C GLY I 169 " pdb=" N PHE I 170 " pdb=" CA PHE I 170 " ideal model delta sigma weight residual 121.54 125.90 -4.36 1.91e+00 2.74e-01 5.22e+00 angle pdb=" C GLY H 169 " pdb=" N PHE H 170 " pdb=" CA PHE H 170 " ideal model delta sigma weight residual 121.54 125.90 -4.36 1.91e+00 2.74e-01 5.21e+00 angle pdb=" C GLY D 169 " pdb=" N PHE D 170 " pdb=" CA PHE D 170 " ideal model delta sigma weight residual 121.54 125.87 -4.33 1.91e+00 2.74e-01 5.15e+00 angle pdb=" C GLY B 169 " pdb=" N PHE B 170 " pdb=" CA PHE B 170 " ideal model delta sigma weight residual 121.54 125.87 -4.33 1.91e+00 2.74e-01 5.14e+00 angle pdb=" C GLY C 169 " pdb=" N PHE C 170 " pdb=" CA PHE C 170 " ideal model delta sigma weight residual 121.54 125.87 -4.33 1.91e+00 2.74e-01 5.13e+00 ... (remaining 59203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 14030 15.43 - 30.85: 1509 30.85 - 46.28: 351 46.28 - 61.70: 190 61.70 - 77.13: 36 Dihedral angle restraints: 16116 sinusoidal: 8292 harmonic: 7824 Sorted by residual: dihedral pdb=" CA ASN C 185 " pdb=" C ASN C 185 " pdb=" N THR C 186 " pdb=" CA THR C 186 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN E 185 " pdb=" C ASN E 185 " pdb=" N THR E 186 " pdb=" CA THR E 186 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN H 185 " pdb=" C ASN H 185 " pdb=" N THR H 186 " pdb=" CA THR H 186 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 16113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1665 0.057 - 0.113: 710 0.113 - 0.170: 304 0.170 - 0.226: 93 0.226 - 0.283: 12 Chirality restraints: 2784 Sorted by residual: chirality pdb=" CB VAL B 187 " pdb=" CA VAL B 187 " pdb=" CG1 VAL B 187 " pdb=" CG2 VAL B 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB VAL F 187 " pdb=" CA VAL F 187 " pdb=" CG1 VAL F 187 " pdb=" CG2 VAL F 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL L 187 " pdb=" CA VAL L 187 " pdb=" CG1 VAL L 187 " pdb=" CG2 VAL L 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2781 not shown) Planarity restraints: 5016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 170 " 0.013 2.00e-02 2.50e+03 1.10e-02 2.11e+00 pdb=" CG PHE H 170 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE H 170 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE H 170 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE H 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 170 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE H 170 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 170 " 0.012 2.00e-02 2.50e+03 1.09e-02 2.06e+00 pdb=" CG PHE J 170 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE J 170 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE J 170 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE J 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE J 170 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE J 170 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 170 " 0.013 2.00e-02 2.50e+03 1.09e-02 2.06e+00 pdb=" CG PHE K 170 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE K 170 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE K 170 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE K 170 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE K 170 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE K 170 " 0.002 2.00e-02 2.50e+03 ... (remaining 5013 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.41: 13829 2.41 - 2.96: 71702 2.96 - 3.51: 84948 3.51 - 4.05: 106798 4.05 - 4.60: 169481 Nonbonded interactions: 446758 Sorted by model distance: nonbonded pdb=" OD1 ASP G 67 " pdb=" HG1 THR H 195 " model vdw 1.867 2.450 nonbonded pdb=" HG1 THR A 195 " pdb=" OD1 ASP F 67 " model vdw 1.872 2.450 nonbonded pdb=" OD1 ASP I 67 " pdb=" HG1 THR J 195 " model vdw 1.873 2.450 nonbonded pdb=" OD1 ASP E 67 " pdb=" HG1 THR F 195 " model vdw 1.874 2.450 nonbonded pdb=" OD1 ASP B 67 " pdb=" HG1 THR C 195 " model vdw 1.875 2.450 ... (remaining 446753 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: 0.07 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: 2.870 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: 0.170 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.320 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.018 0.107 17916 Z= 0.693 Angle : 0.799 6.363 24444 Z= 0.430 Chirality : 0.076 0.283 2784 Planarity : 0.004 0.027 3000 Dihedral : 12.179 69.979 6180 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.14 % Allowed : 3.14 % Favored : 93.71 % 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: -1.67 (0.17), residues: 2076 helix: -0.23 (0.12), residues: 1536 sheet: -2.44 (0.30), residues: 132 loop : -3.66 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 76 TYR 0.010 0.002 TYR B 146 PHE 0.025 0.003 PHE H 170 TRP 0.010 0.003 TRP G 45 HIS 0.003 0.001 HIS F 17 Details of bonding type rmsd covalent geometry : bond 0.01765 (17880) covalent geometry : angle 0.79958 (24372) SS BOND : bond 0.00472 ( 36) SS BOND : angle 0.59940 ( 72) hydrogen bonds : bond 0.11688 ( 1212) hydrogen bonds : angle 6.52412 ( 3600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 459 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 399 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7679 (mmt90) REVERT: A 158 VAL cc_start: 0.8841 (t) cc_final: 0.8564 (m) REVERT: B 76 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7788 (mmt90) REVERT: B 158 VAL cc_start: 0.8876 (t) cc_final: 0.8555 (m) REVERT: C 76 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7596 (mmt90) REVERT: C 158 VAL cc_start: 0.8799 (t) cc_final: 0.8546 (m) REVERT: D 76 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7714 (mmt90) REVERT: D 158 VAL cc_start: 0.8842 (t) cc_final: 0.8564 (m) REVERT: E 76 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7801 (mmt90) REVERT: E 158 VAL cc_start: 0.8868 (t) cc_final: 0.8554 (m) REVERT: F 76 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7570 (mmt90) REVERT: F 158 VAL cc_start: 0.8803 (t) cc_final: 0.8563 (m) REVERT: G 76 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7637 (mmt90) REVERT: G 158 VAL cc_start: 0.8863 (t) cc_final: 0.8569 (m) REVERT: H 76 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7771 (mmt90) REVERT: H 158 VAL cc_start: 0.8890 (t) cc_final: 0.8557 (m) REVERT: I 76 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7496 (mmt90) REVERT: I 158 VAL cc_start: 0.8810 (t) cc_final: 0.8558 (m) REVERT: J 76 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7644 (mmt90) REVERT: J 158 VAL cc_start: 0.8856 (t) cc_final: 0.8557 (m) REVERT: K 76 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7758 (mmt90) REVERT: K 158 VAL cc_start: 0.8888 (t) cc_final: 0.8562 (m) REVERT: L 76 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7499 (mmt90) REVERT: L 151 ILE cc_start: 0.8841 (pt) cc_final: 0.8627 (tt) REVERT: L 158 VAL cc_start: 0.8850 (t) cc_final: 0.8582 (m) outliers start: 60 outliers final: 36 residues processed: 459 average time/residue: 0.3228 time to fit residues: 211.5260 Evaluate side-chains 334 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 286 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.168870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.135155 restraints weight = 53638.134| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.86 r_work: 0.3310 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17916 Z= 0.130 Angle : 0.534 4.669 24444 Z= 0.281 Chirality : 0.038 0.145 2784 Planarity : 0.004 0.027 3000 Dihedral : 7.568 45.299 2400 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.41 % Allowed : 8.96 % Favored : 87.63 % 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: -0.10 (0.18), residues: 2076 helix: 0.90 (0.12), residues: 1548 sheet: -1.77 (0.39), residues: 132 loop : -3.20 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 76 TYR 0.011 0.002 TYR E 66 PHE 0.008 0.001 PHE J 200 TRP 0.004 0.001 TRP E 4 HIS 0.005 0.001 HIS I 221 Details of bonding type rmsd covalent geometry : bond 0.00279 (17880) covalent geometry : angle 0.53053 (24372) SS BOND : bond 0.00133 ( 36) SS BOND : angle 1.19535 ( 72) hydrogen bonds : bond 0.03518 ( 1212) hydrogen bonds : angle 4.53960 ( 3600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 365 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 300 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8917 (mt) cc_final: 0.8577 (tt) REVERT: A 158 VAL cc_start: 0.8766 (t) cc_final: 0.8484 (m) REVERT: B 151 ILE cc_start: 0.8907 (mt) cc_final: 0.8569 (tt) REVERT: B 158 VAL cc_start: 0.8788 (t) cc_final: 0.8458 (m) REVERT: C 17 HIS cc_start: 0.7172 (m90) cc_final: 0.6801 (m90) REVERT: C 158 VAL cc_start: 0.8813 (t) cc_final: 0.8508 (m) REVERT: C 186 THR cc_start: 0.9104 (m) cc_final: 0.8826 (t) REVERT: D 158 VAL cc_start: 0.8775 (t) cc_final: 0.8486 (m) REVERT: E 16 GLU cc_start: 0.6815 (mp0) cc_final: 0.6554 (mp0) REVERT: E 17 HIS cc_start: 0.7225 (m90) cc_final: 0.6805 (m90) REVERT: E 151 ILE cc_start: 0.8900 (mt) cc_final: 0.8527 (tt) REVERT: E 158 VAL cc_start: 0.8793 (t) cc_final: 0.8474 (m) REVERT: F 17 HIS cc_start: 0.7176 (m90) cc_final: 0.6803 (m90) REVERT: F 158 VAL cc_start: 0.8775 (t) cc_final: 0.8480 (m) REVERT: G 151 ILE cc_start: 0.8936 (mt) cc_final: 0.8607 (tt) REVERT: G 158 VAL cc_start: 0.8787 (t) cc_final: 0.8488 (m) REVERT: H 151 ILE cc_start: 0.8914 (mt) cc_final: 0.8583 (tt) REVERT: H 158 VAL cc_start: 0.8827 (t) cc_final: 0.8484 (m) REVERT: I 158 VAL cc_start: 0.8814 (t) cc_final: 0.8482 (m) REVERT: I 186 THR cc_start: 0.9148 (m) cc_final: 0.8889 (t) REVERT: J 151 ILE cc_start: 0.8919 (mt) cc_final: 0.8577 (tt) REVERT: J 158 VAL cc_start: 0.8785 (t) cc_final: 0.8489 (m) REVERT: K 151 ILE cc_start: 0.8915 (mt) cc_final: 0.8588 (tt) REVERT: K 158 VAL cc_start: 0.8783 (t) cc_final: 0.8451 (m) REVERT: L 158 VAL cc_start: 0.8810 (t) cc_final: 0.8488 (m) REVERT: L 186 THR cc_start: 0.9131 (m) cc_final: 0.8821 (t) outliers start: 65 outliers final: 52 residues processed: 346 average time/residue: 0.2964 time to fit residues: 153.4116 Evaluate side-chains 342 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 290 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 221 HIS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain K residue 221 HIS Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 156 PHE Chi-restraints excluded: chain L residue 168 TYR Chi-restraints excluded: chain L residue 179 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 156 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.161016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124236 restraints weight = 54572.363| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.95 r_work: 0.3200 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17916 Z= 0.233 Angle : 0.554 5.314 24444 Z= 0.295 Chirality : 0.039 0.120 2784 Planarity : 0.003 0.025 3000 Dihedral : 6.361 46.358 2352 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.88 % Allowed : 10.59 % Favored : 86.53 % 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: 0.67 (0.18), residues: 2076 helix: 1.59 (0.13), residues: 1536 sheet: -1.51 (0.38), residues: 132 loop : -3.42 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 76 TYR 0.010 0.002 TYR J 146 PHE 0.016 0.002 PHE C 170 TRP 0.004 0.001 TRP A 181 HIS 0.005 0.001 HIS I 221 Details of bonding type rmsd covalent geometry : bond 0.00546 (17880) covalent geometry : angle 0.55296 (24372) SS BOND : bond 0.00414 ( 36) SS BOND : angle 0.93684 ( 72) hydrogen bonds : bond 0.03343 ( 1212) hydrogen bonds : angle 4.52175 ( 3600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 391 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 336 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.7349 (m90) cc_final: 0.7008 (m90) REVERT: A 151 ILE cc_start: 0.8944 (mt) cc_final: 0.8686 (tt) REVERT: A 158 VAL cc_start: 0.8872 (t) cc_final: 0.8557 (m) REVERT: B 16 GLU cc_start: 0.7079 (mp0) cc_final: 0.6783 (mp0) REVERT: B 17 HIS cc_start: 0.7170 (m90) cc_final: 0.6868 (m90) REVERT: B 151 ILE cc_start: 0.8945 (mt) cc_final: 0.8636 (tt) REVERT: B 158 VAL cc_start: 0.8882 (t) cc_final: 0.8507 (m) REVERT: C 17 HIS cc_start: 0.7315 (m90) cc_final: 0.7012 (m90) REVERT: C 158 VAL cc_start: 0.8889 (t) cc_final: 0.8557 (m) REVERT: D 17 HIS cc_start: 0.7323 (m90) cc_final: 0.6992 (m90) REVERT: D 158 VAL cc_start: 0.8867 (t) cc_final: 0.8544 (m) REVERT: E 17 HIS cc_start: 0.7216 (m90) cc_final: 0.6883 (m90) REVERT: E 151 ILE cc_start: 0.8940 (mt) cc_final: 0.8602 (tt) REVERT: E 158 VAL cc_start: 0.8880 (t) cc_final: 0.8531 (m) REVERT: F 17 HIS cc_start: 0.7337 (m90) cc_final: 0.7043 (m90) REVERT: F 158 VAL cc_start: 0.8880 (t) cc_final: 0.8550 (m) REVERT: G 17 HIS cc_start: 0.7348 (m90) cc_final: 0.7022 (m90) REVERT: G 151 ILE cc_start: 0.8948 (mt) cc_final: 0.8704 (tt) REVERT: G 158 VAL cc_start: 0.8893 (t) cc_final: 0.8562 (m) REVERT: H 17 HIS cc_start: 0.7195 (m90) cc_final: 0.6893 (m90) REVERT: H 151 ILE cc_start: 0.8945 (mt) cc_final: 0.8627 (tt) REVERT: H 158 VAL cc_start: 0.8882 (t) cc_final: 0.8518 (m) REVERT: I 158 VAL cc_start: 0.8894 (t) cc_final: 0.8544 (m) REVERT: J 17 HIS cc_start: 0.7324 (m90) cc_final: 0.6999 (m90) REVERT: J 151 ILE cc_start: 0.8962 (mt) cc_final: 0.8704 (tt) REVERT: J 158 VAL cc_start: 0.8862 (t) cc_final: 0.8527 (m) REVERT: K 16 GLU cc_start: 0.7004 (mp0) cc_final: 0.6590 (mp0) REVERT: K 17 HIS cc_start: 0.7202 (m90) cc_final: 0.6842 (m90) REVERT: K 151 ILE cc_start: 0.8941 (mt) cc_final: 0.8636 (tt) REVERT: K 158 VAL cc_start: 0.8868 (t) cc_final: 0.8484 (m) REVERT: L 17 HIS cc_start: 0.7304 (m90) cc_final: 0.6970 (m90) REVERT: L 158 VAL cc_start: 0.8893 (t) cc_final: 0.8551 (m) outliers start: 55 outliers final: 48 residues processed: 363 average time/residue: 0.2932 time to fit residues: 159.1113 Evaluate side-chains 379 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 331 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 57 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.162237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126398 restraints weight = 53900.299| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.89 r_work: 0.3264 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 17916 Z= 0.166 Angle : 0.505 4.851 24444 Z= 0.263 Chirality : 0.038 0.129 2784 Planarity : 0.003 0.026 3000 Dihedral : 6.143 46.055 2352 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.62 % Allowed : 11.11 % Favored : 86.27 % 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: 1.26 (0.19), residues: 2076 helix: 1.96 (0.13), residues: 1536 sheet: -1.08 (0.41), residues: 132 loop : -3.06 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 33 TYR 0.009 0.001 TYR C 146 PHE 0.012 0.001 PHE J 200 TRP 0.004 0.001 TRP L 181 HIS 0.006 0.001 HIS I 221 Details of bonding type rmsd covalent geometry : bond 0.00383 (17880) covalent geometry : angle 0.50441 (24372) SS BOND : bond 0.00302 ( 36) SS BOND : angle 0.70828 ( 72) hydrogen bonds : bond 0.02955 ( 1212) hydrogen bonds : angle 4.28104 ( 3600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 417 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 367 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8992 (mt) cc_final: 0.8755 (tt) REVERT: B 33 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8375 (mtt90) REVERT: B 151 ILE cc_start: 0.8985 (mt) cc_final: 0.8702 (tt) REVERT: B 158 VAL cc_start: 0.8879 (t) cc_final: 0.8519 (m) REVERT: C 151 ILE cc_start: 0.8972 (mt) cc_final: 0.8727 (tt) REVERT: C 158 VAL cc_start: 0.8912 (t) cc_final: 0.8582 (m) REVERT: E 151 ILE cc_start: 0.8989 (mt) cc_final: 0.8681 (tt) REVERT: E 158 VAL cc_start: 0.8929 (t) cc_final: 0.8572 (m) REVERT: F 151 ILE cc_start: 0.8968 (mt) cc_final: 0.8708 (tt) REVERT: F 158 VAL cc_start: 0.8914 (t) cc_final: 0.8581 (m) REVERT: G 151 ILE cc_start: 0.9006 (mt) cc_final: 0.8780 (tt) REVERT: H 151 ILE cc_start: 0.8981 (mt) cc_final: 0.8697 (tt) REVERT: H 158 VAL cc_start: 0.8918 (t) cc_final: 0.8518 (m) REVERT: J 151 ILE cc_start: 0.8981 (mt) cc_final: 0.8747 (tt) REVERT: K 33 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8359 (mtt90) REVERT: K 151 ILE cc_start: 0.8980 (mt) cc_final: 0.8663 (tt) REVERT: K 158 VAL cc_start: 0.8878 (t) cc_final: 0.8527 (m) outliers start: 50 outliers final: 48 residues processed: 399 average time/residue: 0.2818 time to fit residues: 168.7206 Evaluate side-chains 378 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 328 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 33 ARG Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 44 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 HIS D 17 HIS H 17 HIS K 17 HIS L 17 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.161588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.125448 restraints weight = 54331.083| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.99 r_work: 0.3138 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 17916 Z= 0.154 Angle : 0.494 4.794 24444 Z= 0.258 Chirality : 0.037 0.119 2784 Planarity : 0.003 0.026 3000 Dihedral : 6.056 46.195 2352 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.94 % Allowed : 12.05 % Favored : 85.01 % 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: 1.53 (0.19), residues: 2076 helix: 2.18 (0.13), residues: 1536 sheet: -0.86 (0.43), residues: 132 loop : -3.10 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 33 TYR 0.008 0.001 TYR H 146 PHE 0.013 0.001 PHE A 200 TRP 0.004 0.001 TRP G 181 HIS 0.005 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00359 (17880) covalent geometry : angle 0.49347 (24372) SS BOND : bond 0.00318 ( 36) SS BOND : angle 0.66737 ( 72) hydrogen bonds : bond 0.02871 ( 1212) hydrogen bonds : angle 4.22804 ( 3600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 411 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 355 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8955 (mt) cc_final: 0.8733 (tt) REVERT: A 158 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8405 (m) REVERT: B 151 ILE cc_start: 0.8969 (mt) cc_final: 0.8696 (tt) REVERT: B 158 VAL cc_start: 0.8841 (t) cc_final: 0.8483 (m) REVERT: C 151 ILE cc_start: 0.8929 (mt) cc_final: 0.8687 (tt) REVERT: C 158 VAL cc_start: 0.8881 (t) cc_final: 0.8543 (m) REVERT: D 151 ILE cc_start: 0.8948 (mt) cc_final: 0.8635 (tt) REVERT: D 158 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8403 (m) REVERT: E 151 ILE cc_start: 0.8956 (mt) cc_final: 0.8669 (tt) REVERT: E 158 VAL cc_start: 0.8871 (t) cc_final: 0.8486 (m) REVERT: F 151 ILE cc_start: 0.8940 (mt) cc_final: 0.8690 (tt) REVERT: F 158 VAL cc_start: 0.8874 (t) cc_final: 0.8531 (m) REVERT: G 151 ILE cc_start: 0.8970 (mt) cc_final: 0.8765 (tt) REVERT: G 158 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8425 (m) REVERT: H 151 ILE cc_start: 0.8943 (mt) cc_final: 0.8708 (tt) REVERT: H 158 VAL cc_start: 0.8854 (t) cc_final: 0.8472 (m) REVERT: J 151 ILE cc_start: 0.8948 (mt) cc_final: 0.8734 (tt) REVERT: K 151 ILE cc_start: 0.8954 (mt) cc_final: 0.8689 (tt) REVERT: K 158 VAL cc_start: 0.8827 (t) cc_final: 0.8470 (m) outliers start: 56 outliers final: 48 residues processed: 388 average time/residue: 0.2750 time to fit residues: 159.8218 Evaluate side-chains 390 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 339 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.152738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.116162 restraints weight = 55576.386| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.99 r_work: 0.3055 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 17916 Z= 0.327 Angle : 0.596 5.201 24444 Z= 0.324 Chirality : 0.042 0.276 2784 Planarity : 0.004 0.034 3000 Dihedral : 6.411 48.691 2352 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.72 % Allowed : 12.58 % Favored : 83.70 % 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: 1.32 (0.19), residues: 2076 helix: 2.04 (0.13), residues: 1536 sheet: -0.72 (0.43), residues: 132 loop : -3.34 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 76 TYR 0.011 0.002 TYR D 176 PHE 0.021 0.002 PHE H 170 TRP 0.006 0.001 TRP E 45 HIS 0.005 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00762 (17880) covalent geometry : angle 0.59496 (24372) SS BOND : bond 0.00663 ( 36) SS BOND : angle 0.76953 ( 72) hydrogen bonds : bond 0.03351 ( 1212) hydrogen bonds : angle 4.59017 ( 3600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 450 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 379 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8473 (mtt90) REVERT: B 151 ILE cc_start: 0.8966 (mt) cc_final: 0.8753 (tt) REVERT: B 158 VAL cc_start: 0.8949 (t) cc_final: 0.8737 (m) REVERT: C 151 ILE cc_start: 0.8964 (mt) cc_final: 0.8730 (tt) REVERT: D 151 ILE cc_start: 0.8993 (mt) cc_final: 0.8715 (tt) REVERT: E 33 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8424 (mtt90) REVERT: E 151 ILE cc_start: 0.8978 (mt) cc_final: 0.8749 (tt) REVERT: E 158 VAL cc_start: 0.8936 (t) cc_final: 0.8556 (m) REVERT: F 151 ILE cc_start: 0.8959 (mt) cc_final: 0.8708 (tt) REVERT: F 158 VAL cc_start: 0.8955 (t) cc_final: 0.8606 (m) REVERT: H 33 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8430 (mtt90) REVERT: H 151 ILE cc_start: 0.8946 (mt) cc_final: 0.8743 (tt) REVERT: H 158 VAL cc_start: 0.8938 (t) cc_final: 0.8718 (m) REVERT: I 218 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7824 (mm-30) REVERT: K 151 ILE cc_start: 0.8969 (mt) cc_final: 0.8764 (tt) REVERT: K 158 VAL cc_start: 0.8931 (t) cc_final: 0.8714 (m) outliers start: 71 outliers final: 61 residues processed: 413 average time/residue: 0.2524 time to fit residues: 160.2646 Evaluate side-chains 389 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 325 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 7 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 63 optimal weight: 0.2980 chunk 70 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 HIS J 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.158264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.122208 restraints weight = 54251.519| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.00 r_work: 0.3097 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17916 Z= 0.137 Angle : 0.499 4.857 24444 Z= 0.260 Chirality : 0.037 0.180 2784 Planarity : 0.003 0.029 3000 Dihedral : 6.281 47.733 2352 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.25 % Allowed : 14.36 % Favored : 82.39 % 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: 1.84 (0.19), residues: 2076 helix: 2.40 (0.13), residues: 1536 sheet: -0.67 (0.45), residues: 132 loop : -3.04 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 9 TYR 0.013 0.002 TYR G 146 PHE 0.014 0.001 PHE J 200 TRP 0.006 0.001 TRP L 181 HIS 0.006 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00321 (17880) covalent geometry : angle 0.49798 (24372) SS BOND : bond 0.00311 ( 36) SS BOND : angle 0.74713 ( 72) hydrogen bonds : bond 0.02920 ( 1212) hydrogen bonds : angle 4.23638 ( 3600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 411 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 349 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8446 (mtt90) REVERT: B 158 VAL cc_start: 0.9022 (t) cc_final: 0.8664 (m) REVERT: C 158 VAL cc_start: 0.8737 (p) cc_final: 0.8448 (m) REVERT: E 158 VAL cc_start: 0.8860 (t) cc_final: 0.8488 (m) REVERT: F 158 VAL cc_start: 0.8890 (t) cc_final: 0.8531 (m) REVERT: F 220 TYR cc_start: 0.7551 (m-10) cc_final: 0.7259 (m-10) REVERT: H 158 VAL cc_start: 0.9041 (t) cc_final: 0.8677 (m) REVERT: K 158 VAL cc_start: 0.9034 (t) cc_final: 0.8663 (m) outliers start: 62 outliers final: 55 residues processed: 375 average time/residue: 0.2723 time to fit residues: 154.5231 Evaluate side-chains 399 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 343 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 7 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 150 optimal weight: 0.4980 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 17 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.158774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.122930 restraints weight = 53808.577| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.97 r_work: 0.3112 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17916 Z= 0.134 Angle : 0.488 4.809 24444 Z= 0.253 Chirality : 0.037 0.162 2784 Planarity : 0.003 0.027 3000 Dihedral : 6.207 47.229 2352 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.88 % Allowed : 14.57 % Favored : 82.55 % 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: 2.00 (0.19), residues: 2076 helix: 2.52 (0.13), residues: 1536 sheet: -0.68 (0.45), residues: 132 loop : -2.93 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 33 TYR 0.010 0.001 TYR A 146 PHE 0.013 0.001 PHE G 200 TRP 0.005 0.001 TRP L 181 HIS 0.006 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00313 (17880) covalent geometry : angle 0.48738 (24372) SS BOND : bond 0.00292 ( 36) SS BOND : angle 0.68267 ( 72) hydrogen bonds : bond 0.02786 ( 1212) hydrogen bonds : angle 4.13003 ( 3600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 421 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 366 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8446 (mtt90) REVERT: B 158 VAL cc_start: 0.9017 (t) cc_final: 0.8663 (m) REVERT: C 158 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8452 (m) REVERT: C 220 TYR cc_start: 0.7497 (m-10) cc_final: 0.7198 (m-10) REVERT: E 158 VAL cc_start: 0.8856 (t) cc_final: 0.8483 (m) REVERT: F 158 VAL cc_start: 0.8877 (t) cc_final: 0.8519 (m) REVERT: F 220 TYR cc_start: 0.7475 (m-10) cc_final: 0.7173 (m-10) REVERT: H 158 VAL cc_start: 0.9027 (t) cc_final: 0.8675 (m) REVERT: K 158 VAL cc_start: 0.9028 (t) cc_final: 0.8658 (m) outliers start: 55 outliers final: 48 residues processed: 387 average time/residue: 0.2821 time to fit residues: 162.6367 Evaluate side-chains 409 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 359 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 43 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 184 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.160628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124653 restraints weight = 53672.668| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.01 r_work: 0.3117 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17916 Z= 0.126 Angle : 0.487 6.633 24444 Z= 0.251 Chirality : 0.037 0.256 2784 Planarity : 0.003 0.022 3000 Dihedral : 5.981 46.688 2344 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.46 % Allowed : 15.36 % Favored : 82.18 % 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: 2.06 (0.19), residues: 2076 helix: 2.59 (0.13), residues: 1536 sheet: -0.98 (0.44), residues: 132 loop : -2.91 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 33 TYR 0.011 0.001 TYR B 146 PHE 0.014 0.001 PHE J 32 TRP 0.005 0.001 TRP L 181 HIS 0.006 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00289 (17880) covalent geometry : angle 0.48624 (24372) SS BOND : bond 0.00258 ( 36) SS BOND : angle 0.64807 ( 72) hydrogen bonds : bond 0.02696 ( 1212) hydrogen bonds : angle 4.04621 ( 3600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 426 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 379 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8420 (mtt90) REVERT: B 158 VAL cc_start: 0.9013 (t) cc_final: 0.8658 (m) REVERT: C 158 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8437 (m) REVERT: C 218 GLU cc_start: 0.8111 (tt0) cc_final: 0.7806 (tt0) REVERT: C 220 TYR cc_start: 0.7559 (m-10) cc_final: 0.7257 (m-10) REVERT: E 158 VAL cc_start: 0.8841 (t) cc_final: 0.8466 (m) REVERT: F 158 VAL cc_start: 0.8876 (t) cc_final: 0.8510 (m) REVERT: F 218 GLU cc_start: 0.8045 (tt0) cc_final: 0.7752 (tt0) REVERT: F 220 TYR cc_start: 0.7512 (m-10) cc_final: 0.7208 (m-10) REVERT: H 158 VAL cc_start: 0.9017 (t) cc_final: 0.8669 (m) REVERT: H 220 TYR cc_start: 0.7545 (m-10) cc_final: 0.7270 (m-10) REVERT: K 158 VAL cc_start: 0.9015 (t) cc_final: 0.8652 (m) REVERT: K 220 TYR cc_start: 0.7566 (m-10) cc_final: 0.7284 (m-10) outliers start: 47 outliers final: 41 residues processed: 399 average time/residue: 0.2891 time to fit residues: 173.1672 Evaluate side-chains 411 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 368 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 146 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 150 optimal weight: 0.0570 chunk 64 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.161348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126385 restraints weight = 54191.679| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.88 r_work: 0.3156 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17916 Z= 0.102 Angle : 0.478 5.520 24444 Z= 0.245 Chirality : 0.036 0.219 2784 Planarity : 0.003 0.024 3000 Dihedral : 5.669 45.525 2328 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.15 % Allowed : 15.93 % Favored : 81.92 % 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: 2.19 (0.19), residues: 2076 helix: 2.72 (0.13), residues: 1536 sheet: -1.09 (0.42), residues: 132 loop : -2.92 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 144 TYR 0.011 0.001 TYR J 146 PHE 0.012 0.001 PHE G 200 TRP 0.006 0.001 TRP G 181 HIS 0.006 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00230 (17880) covalent geometry : angle 0.47763 (24372) SS BOND : bond 0.00178 ( 36) SS BOND : angle 0.68146 ( 72) hydrogen bonds : bond 0.02594 ( 1212) hydrogen bonds : angle 3.94367 ( 3600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Evaluate side-chains 436 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 395 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 VAL cc_start: 0.9043 (t) cc_final: 0.8695 (m) REVERT: B 220 TYR cc_start: 0.7484 (m-10) cc_final: 0.7175 (m-10) REVERT: C 158 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8500 (m) REVERT: C 218 GLU cc_start: 0.8058 (tt0) cc_final: 0.7786 (mm-30) REVERT: C 220 TYR cc_start: 0.7479 (m-10) cc_final: 0.7154 (m-10) REVERT: E 158 VAL cc_start: 0.8871 (t) cc_final: 0.8498 (m) REVERT: E 220 TYR cc_start: 0.7402 (m-10) cc_final: 0.7086 (m-10) REVERT: F 158 VAL cc_start: 0.8882 (t) cc_final: 0.8527 (m) REVERT: F 220 TYR cc_start: 0.7414 (m-10) cc_final: 0.7097 (m-10) REVERT: G 17 HIS cc_start: 0.7236 (m90) cc_final: 0.7032 (m90) REVERT: H 158 VAL cc_start: 0.9030 (t) cc_final: 0.8691 (m) REVERT: H 220 TYR cc_start: 0.7465 (m-10) cc_final: 0.7175 (m-10) REVERT: J 17 HIS cc_start: 0.7310 (m90) cc_final: 0.7102 (m90) REVERT: K 158 VAL cc_start: 0.9044 (t) cc_final: 0.8693 (m) REVERT: K 220 TYR cc_start: 0.7478 (m-10) cc_final: 0.7189 (m-10) outliers start: 41 outliers final: 38 residues processed: 411 average time/residue: 0.2822 time to fit residues: 174.3427 Evaluate side-chains 424 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 385 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 168 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 168 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 168 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 168 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 168 TYR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 168 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 168 TYR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 168 TYR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 168 TYR Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 168 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 154 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.152896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.116691 restraints weight = 55120.631| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.99 r_work: 0.3097 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 17916 Z= 0.170 Angle : 0.501 5.670 24444 Z= 0.261 Chirality : 0.038 0.200 2784 Planarity : 0.003 0.024 3000 Dihedral : 5.717 46.206 2328 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.31 % Allowed : 16.46 % Favored : 81.24 % 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: 2.10 (0.19), residues: 2076 helix: 2.66 (0.13), residues: 1536 sheet: -1.07 (0.42), residues: 132 loop : -3.01 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 144 TYR 0.010 0.001 TYR G 146 PHE 0.014 0.001 PHE G 200 TRP 0.003 0.001 TRP E 45 HIS 0.006 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00398 (17880) covalent geometry : angle 0.50134 (24372) SS BOND : bond 0.00362 ( 36) SS BOND : angle 0.54897 ( 72) hydrogen bonds : bond 0.02695 ( 1212) hydrogen bonds : angle 4.05841 ( 3600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7846.16 seconds wall clock time: 133 minutes 35.31 seconds (8015.31 seconds total)