Starting phenix.real_space_refine on Fri Mar 6 18:25:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z85_11114/03_2026/6z85_11114.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z85_11114/03_2026/6z85_11114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6z85_11114/03_2026/6z85_11114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z85_11114/03_2026/6z85_11114.map" model { file = "/net/cci-nas-00/data/ceres_data/6z85_11114/03_2026/6z85_11114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z85_11114/03_2026/6z85_11114.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 18710 atoms to isotropic. 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 Zn 10 6.06 5 S 130 5.16 5 C 12010 2.51 5 N 3340 2.21 5 O 3390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18880 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1218 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 2 Chain: "K" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 652 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 76} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'HBI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 450 SG CYS A 141 83.878 54.292 79.608 1.00 0.00 S ATOM 1004 SG CYS A 212 81.552 50.817 77.887 1.00 0.00 S Restraints were copied for chains: C, D, B, E, G, H, I, J, F, L, M, N, O, P, Q, R, S, T Time building chain proxies: 1.37, per 1000 atoms: 0.07 Number of scatterers: 18880 At special positions: 0 Unit cell: (110.931, 115.239, 141.087, 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) Zn 10 29.99 S 130 16.00 O 3390 8.00 N 3340 7.00 C 12010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 844.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 141 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 212 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 144 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 141 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 212 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 144 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 141 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 212 " pdb="ZN ZN C 301 " - pdb=" ND1 HIS C 144 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 141 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 212 " pdb="ZN ZN D 301 " - pdb=" ND1 HIS D 144 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 141 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 212 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 144 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 141 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 212 " pdb="ZN ZN F 301 " - pdb=" ND1 HIS F 144 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 141 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 212 " pdb="ZN ZN G 301 " - pdb=" ND1 HIS G 144 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 141 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 212 " pdb="ZN ZN H 301 " - pdb=" ND1 HIS H 144 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 141 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 212 " pdb="ZN ZN I 301 " - pdb=" ND1 HIS I 144 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 141 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 212 " pdb="ZN ZN J 301 " - pdb=" ND1 HIS J 144 " 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4400 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 39.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 67 through 82 removed outlier: 3.523A pdb=" N ALA A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 166 through 177 removed outlier: 3.506A pdb=" N ARG A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 198 removed outlier: 3.526A pdb=" N LYS A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.605A pdb=" N ASP A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 237' Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'K' and resid 25 through 33 Processing helix chain 'K' and resid 52 through 62 removed outlier: 3.580A pdb=" N VAL K 56 " --> pdb=" O PRO K 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG K 62 " --> pdb=" O ASP K 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 33 Processing helix chain 'L' and resid 52 through 62 removed outlier: 3.579A pdb=" N VAL L 56 " --> pdb=" O PRO L 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG L 62 " --> pdb=" O ASP L 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 33 Processing helix chain 'M' and resid 52 through 62 removed outlier: 3.580A pdb=" N VAL M 56 " --> pdb=" O PRO M 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 33 Processing helix chain 'N' and resid 52 through 62 removed outlier: 3.579A pdb=" N VAL N 56 " --> pdb=" O PRO N 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG N 62 " --> pdb=" O ASP N 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 33 Processing helix chain 'O' and resid 52 through 62 removed outlier: 3.580A pdb=" N VAL O 56 " --> pdb=" O PRO O 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG O 62 " --> pdb=" O ASP O 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 33 Processing helix chain 'P' and resid 52 through 62 removed outlier: 3.580A pdb=" N VAL P 56 " --> pdb=" O PRO P 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG P 62 " --> pdb=" O ASP P 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 33 Processing helix chain 'Q' and resid 52 through 62 removed outlier: 3.580A pdb=" N VAL Q 56 " --> pdb=" O PRO Q 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG Q 62 " --> pdb=" O ASP Q 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 33 Processing helix chain 'R' and resid 52 through 62 removed outlier: 3.580A pdb=" N VAL R 56 " --> pdb=" O PRO R 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG R 62 " --> pdb=" O ASP R 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 33 Processing helix chain 'S' and resid 52 through 62 removed outlier: 3.579A pdb=" N VAL S 56 " --> pdb=" O PRO S 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG S 62 " --> pdb=" O ASP S 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 33 Processing helix chain 'T' and resid 52 through 62 removed outlier: 3.580A pdb=" N VAL T 56 " --> pdb=" O PRO T 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG T 62 " --> pdb=" O ASP T 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 82 removed outlier: 3.523A pdb=" N ALA C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 166 through 177 removed outlier: 3.506A pdb=" N ARG C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 198 removed outlier: 3.526A pdb=" N LYS C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 237 removed outlier: 3.605A pdb=" N ASP C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 233 through 237' Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'D' and resid 68 through 82 removed outlier: 3.524A pdb=" N ALA D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 103 Processing helix chain 'D' and resid 166 through 177 removed outlier: 3.506A pdb=" N ARG D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 198 removed outlier: 3.526A pdb=" N LYS D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.606A pdb=" N ASP D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 237' Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'B' and resid 68 through 82 removed outlier: 3.523A pdb=" N ALA B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 103 Processing helix chain 'B' and resid 166 through 177 removed outlier: 3.506A pdb=" N ARG B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 198 removed outlier: 3.525A pdb=" N LYS B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.604A pdb=" N ASP B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 233 through 237' Processing helix chain 'B' and resid 237 through 248 Processing helix chain 'E' and resid 68 through 82 removed outlier: 3.523A pdb=" N ALA E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 103 Processing helix chain 'E' and resid 166 through 177 removed outlier: 3.506A pdb=" N ARG E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 198 removed outlier: 3.526A pdb=" N LYS E 187 " --> pdb=" O GLU E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 237 removed outlier: 3.605A pdb=" N ASP E 237 " --> pdb=" O VAL E 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 233 through 237' Processing helix chain 'E' and resid 237 through 248 Processing helix chain 'G' and resid 68 through 82 removed outlier: 3.524A pdb=" N ALA G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 103 Processing helix chain 'G' and resid 166 through 177 removed outlier: 3.506A pdb=" N ARG G 170 " --> pdb=" O SER G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 198 removed outlier: 3.526A pdb=" N LYS G 187 " --> pdb=" O GLU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 237 removed outlier: 3.605A pdb=" N ASP G 237 " --> pdb=" O VAL G 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 233 through 237' Processing helix chain 'G' and resid 237 through 248 Processing helix chain 'H' and resid 68 through 82 removed outlier: 3.523A pdb=" N ALA H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 103 Processing helix chain 'H' and resid 166 through 177 removed outlier: 3.506A pdb=" N ARG H 170 " --> pdb=" O SER H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 198 removed outlier: 3.526A pdb=" N LYS H 187 " --> pdb=" O GLU H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 237 removed outlier: 3.605A pdb=" N ASP H 237 " --> pdb=" O VAL H 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 233 through 237' Processing helix chain 'H' and resid 237 through 248 Processing helix chain 'I' and resid 68 through 82 removed outlier: 3.524A pdb=" N ALA I 74 " --> pdb=" O ASN I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 103 Processing helix chain 'I' and resid 166 through 177 removed outlier: 3.507A pdb=" N ARG I 170 " --> pdb=" O SER I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 198 removed outlier: 3.526A pdb=" N LYS I 187 " --> pdb=" O GLU I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 237 removed outlier: 3.605A pdb=" N ASP I 237 " --> pdb=" O VAL I 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 233 through 237' Processing helix chain 'I' and resid 237 through 248 Processing helix chain 'J' and resid 68 through 82 removed outlier: 3.523A pdb=" N ALA J 74 " --> pdb=" O ASN J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 103 Processing helix chain 'J' and resid 166 through 177 removed outlier: 3.506A pdb=" N ARG J 170 " --> pdb=" O SER J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 198 removed outlier: 3.526A pdb=" N LYS J 187 " --> pdb=" O GLU J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 237 removed outlier: 3.606A pdb=" N ASP J 237 " --> pdb=" O VAL J 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 233 through 237' Processing helix chain 'J' and resid 237 through 248 Processing helix chain 'F' and resid 68 through 82 removed outlier: 3.524A pdb=" N ALA F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 103 Processing helix chain 'F' and resid 166 through 177 removed outlier: 3.507A pdb=" N ARG F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 198 removed outlier: 3.525A pdb=" N LYS F 187 " --> pdb=" O GLU F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 237 removed outlier: 3.605A pdb=" N ASP F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 233 through 237' Processing helix chain 'F' and resid 237 through 248 551 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5043 1.33 - 1.45: 3131 1.45 - 1.57: 10816 1.57 - 1.69: 0 1.69 - 1.81: 230 Bond restraints: 19220 Sorted by residual: bond pdb=" C4A HBI D 302 " pdb=" C8A HBI D 302 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" C4A HBI B 302 " pdb=" C8A HBI B 302 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.46e+00 bond pdb=" C4A HBI J 302 " pdb=" C8A HBI J 302 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C4A HBI F 302 " pdb=" C8A HBI F 302 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C4A HBI I 302 " pdb=" C8A HBI I 302 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.35e+00 ... (remaining 19215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 23761 1.78 - 3.56: 1896 3.56 - 5.34: 273 5.34 - 7.12: 20 7.12 - 8.90: 10 Bond angle restraints: 25960 Sorted by residual: angle pdb=" N GLY I 150 " pdb=" CA GLY I 150 " pdb=" C GLY I 150 " ideal model delta sigma weight residual 111.66 118.57 -6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" N GLY G 150 " pdb=" CA GLY G 150 " pdb=" C GLY G 150 " ideal model delta sigma weight residual 111.66 118.55 -6.89 1.91e+00 2.74e-01 1.30e+01 angle pdb=" N GLY H 150 " pdb=" CA GLY H 150 " pdb=" C GLY H 150 " ideal model delta sigma weight residual 111.66 118.55 -6.89 1.91e+00 2.74e-01 1.30e+01 angle pdb=" N GLY J 150 " pdb=" CA GLY J 150 " pdb=" C GLY J 150 " ideal model delta sigma weight residual 111.66 118.55 -6.89 1.91e+00 2.74e-01 1.30e+01 angle pdb=" N GLY D 150 " pdb=" CA GLY D 150 " pdb=" C GLY D 150 " ideal model delta sigma weight residual 111.66 118.54 -6.88 1.91e+00 2.74e-01 1.30e+01 ... (remaining 25955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 11128 14.52 - 29.03: 482 29.03 - 43.54: 90 43.54 - 58.06: 40 58.06 - 72.57: 10 Dihedral angle restraints: 11750 sinusoidal: 4950 harmonic: 6800 Sorted by residual: dihedral pdb=" CA GLN G 180 " pdb=" C GLN G 180 " pdb=" N VAL G 181 " pdb=" CA VAL G 181 " ideal model delta harmonic sigma weight residual 180.00 148.46 31.54 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA GLN H 180 " pdb=" C GLN H 180 " pdb=" N VAL H 181 " pdb=" CA VAL H 181 " ideal model delta harmonic sigma weight residual 180.00 148.46 31.54 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA GLN B 180 " pdb=" C GLN B 180 " pdb=" N VAL B 181 " pdb=" CA VAL B 181 " ideal model delta harmonic sigma weight residual 180.00 148.47 31.53 0 5.00e+00 4.00e-02 3.98e+01 ... (remaining 11747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1955 0.053 - 0.106: 762 0.106 - 0.159: 203 0.159 - 0.212: 30 0.212 - 0.265: 20 Chirality restraints: 2970 Sorted by residual: chirality pdb=" CB THR L 17 " pdb=" CA THR L 17 " pdb=" OG1 THR L 17 " pdb=" CG2 THR L 17 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB THR N 17 " pdb=" CA THR N 17 " pdb=" OG1 THR N 17 " pdb=" CG2 THR N 17 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB THR O 17 " pdb=" CA THR O 17 " pdb=" OG1 THR O 17 " pdb=" CG2 THR O 17 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2967 not shown) Planarity restraints: 3260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 HBI B 302 " -0.007 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" C4 HBI B 302 " 0.018 2.00e-02 2.50e+03 pdb=" C4A HBI B 302 " 0.006 2.00e-02 2.50e+03 pdb=" C8A HBI B 302 " -0.006 2.00e-02 2.50e+03 pdb=" N1 HBI B 302 " -0.030 2.00e-02 2.50e+03 pdb=" N2 HBI B 302 " -0.006 2.00e-02 2.50e+03 pdb=" N3 HBI B 302 " 0.017 2.00e-02 2.50e+03 pdb=" N5 HBI B 302 " -0.044 2.00e-02 2.50e+03 pdb=" N8 HBI B 302 " 0.044 2.00e-02 2.50e+03 pdb=" O4 HBI B 302 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 HBI I 302 " -0.007 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" C4 HBI I 302 " 0.018 2.00e-02 2.50e+03 pdb=" C4A HBI I 302 " 0.006 2.00e-02 2.50e+03 pdb=" C8A HBI I 302 " -0.006 2.00e-02 2.50e+03 pdb=" N1 HBI I 302 " -0.029 2.00e-02 2.50e+03 pdb=" N2 HBI I 302 " -0.007 2.00e-02 2.50e+03 pdb=" N3 HBI I 302 " 0.017 2.00e-02 2.50e+03 pdb=" N5 HBI I 302 " -0.044 2.00e-02 2.50e+03 pdb=" N8 HBI I 302 " 0.043 2.00e-02 2.50e+03 pdb=" O4 HBI I 302 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 HBI A 302 " 0.007 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" C4 HBI A 302 " -0.018 2.00e-02 2.50e+03 pdb=" C4A HBI A 302 " -0.006 2.00e-02 2.50e+03 pdb=" C8A HBI A 302 " 0.005 2.00e-02 2.50e+03 pdb=" N1 HBI A 302 " 0.030 2.00e-02 2.50e+03 pdb=" N2 HBI A 302 " 0.006 2.00e-02 2.50e+03 pdb=" N3 HBI A 302 " -0.017 2.00e-02 2.50e+03 pdb=" N5 HBI A 302 " 0.044 2.00e-02 2.50e+03 pdb=" N8 HBI A 302 " -0.043 2.00e-02 2.50e+03 pdb=" O4 HBI A 302 " -0.008 2.00e-02 2.50e+03 ... (remaining 3257 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5435 2.82 - 3.34: 15722 3.34 - 3.86: 30516 3.86 - 4.38: 38604 4.38 - 4.90: 66126 Nonbonded interactions: 156403 Sorted by model distance: nonbonded pdb=" OE1 GLN F 182 " pdb=" OG1 THR F 225 " model vdw 2.301 3.040 nonbonded pdb=" OE1 GLN A 182 " pdb=" OG1 THR A 225 " model vdw 2.301 3.040 nonbonded pdb=" OE1 GLN D 182 " pdb=" OG1 THR D 225 " model vdw 2.301 3.040 nonbonded pdb=" OE1 GLN B 182 " pdb=" OG1 THR B 225 " model vdw 2.301 3.040 nonbonded pdb=" OE1 GLN C 182 " pdb=" OG1 THR C 225 " model vdw 2.301 3.040 ... (remaining 156398 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'F' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.200 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 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 : 0.017 0.552 19250 Z= 0.592 Angle : 1.048 8.904 25960 Z= 0.585 Chirality : 0.062 0.265 2970 Planarity : 0.008 0.052 3260 Dihedral : 9.840 72.575 7350 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.49 % Allowed : 1.46 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -4.47 (0.13), residues: 2280 helix: -4.21 (0.08), residues: 880 sheet: -0.71 (0.19), residues: 660 loop : -3.14 (0.16), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 241 TYR 0.026 0.004 TYR G 75 PHE 0.043 0.005 PHE F 234 TRP 0.005 0.002 TRP O 79 HIS 0.008 0.002 HIS D 210 Details of bonding type rmsd covalent geometry : bond 0.00905 (19220) covalent geometry : angle 1.04802 (25960) hydrogen bonds : bond 0.34261 ( 551) hydrogen bonds : angle 10.28941 ( 1653) metal coordination : bond 0.35286 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 487 time to evaluate : 0.730 Fit side-chains REVERT: A 242 GLU cc_start: 0.7221 (tt0) cc_final: 0.6657 (tt0) REVERT: C 137 MET cc_start: 0.7250 (tmm) cc_final: 0.7018 (tmm) REVERT: C 143 HIS cc_start: 0.7407 (m170) cc_final: 0.7156 (m-70) REVERT: C 177 ARG cc_start: 0.7695 (mmt180) cc_final: 0.7180 (mpt180) REVERT: D 225 THR cc_start: 0.8356 (p) cc_final: 0.8049 (m) REVERT: B 177 ARG cc_start: 0.7541 (mmt180) cc_final: 0.6915 (mpt180) REVERT: B 194 THR cc_start: 0.8476 (m) cc_final: 0.8207 (m) REVERT: E 168 LEU cc_start: 0.8168 (mt) cc_final: 0.7958 (tp) REVERT: E 225 THR cc_start: 0.7888 (p) cc_final: 0.7635 (m) REVERT: E 242 GLU cc_start: 0.7238 (tt0) cc_final: 0.6829 (OUTLIER) REVERT: G 225 THR cc_start: 0.7981 (p) cc_final: 0.7585 (m) REVERT: H 225 THR cc_start: 0.8131 (p) cc_final: 0.7827 (m) REVERT: H 237 ASP cc_start: 0.7954 (t0) cc_final: 0.7748 (t0) REVERT: I 225 THR cc_start: 0.8425 (p) cc_final: 0.8139 (m) REVERT: J 225 THR cc_start: 0.7938 (p) cc_final: 0.7689 (m) REVERT: F 97 ARG cc_start: 0.7312 (mtt90) cc_final: 0.7091 (mtt90) REVERT: F 225 THR cc_start: 0.8071 (p) cc_final: 0.7553 (m) REVERT: F 242 GLU cc_start: 0.7153 (tt0) cc_final: 0.6694 (mt-10) outliers start: 10 outliers final: 10 residues processed: 497 average time/residue: 0.5848 time to fit residues: 326.8011 Evaluate side-chains 398 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 389 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 ASN L 42 ASN M 42 ASN N 42 ASN O 42 ASN P 42 ASN Q 42 ASN R 42 ASN S 42 ASN T 42 ASN C 180 GLN D 180 GLN D 188 GLN B 143 HIS H 143 HIS H 180 GLN I 180 GLN J 143 HIS J 180 GLN F 143 HIS F 180 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.244581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.220970 restraints weight = 15569.672| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 1.11 r_work: 0.4231 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4121 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19250 Z= 0.136 Angle : 0.543 6.278 25960 Z= 0.281 Chirality : 0.044 0.128 2970 Planarity : 0.005 0.044 3260 Dihedral : 6.961 41.189 2720 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.33 % Allowed : 10.10 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.93 (0.16), residues: 2280 helix: -1.17 (0.16), residues: 880 sheet: -0.18 (0.20), residues: 670 loop : -2.27 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 97 TYR 0.012 0.002 TYR J 156 PHE 0.020 0.002 PHE A 148 TRP 0.004 0.001 TRP A 96 HIS 0.010 0.001 HIS N 31 Details of bonding type rmsd covalent geometry : bond 0.00318 (19220) covalent geometry : angle 0.54258 (25960) hydrogen bonds : bond 0.04791 ( 551) hydrogen bonds : angle 4.75112 ( 1653) metal coordination : bond 0.01078 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 380 time to evaluate : 0.716 Fit side-chains REVERT: A 211 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6493 (OUTLIER) REVERT: K 54 ARG cc_start: 0.6493 (ttp-110) cc_final: 0.6109 (ttm110) REVERT: L 37 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7345 (ttp-170) REVERT: N 18 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.6648 (mmt) REVERT: N 23 GLN cc_start: 0.7004 (mt0) cc_final: 0.6789 (pt0) REVERT: N 37 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7000 (ptt90) REVERT: O 29 MET cc_start: 0.6995 (mmp) cc_final: 0.6399 (mmp) REVERT: O 51 ASP cc_start: 0.7463 (m-30) cc_final: 0.7234 (m-30) REVERT: T 51 ASP cc_start: 0.7363 (m-30) cc_final: 0.7130 (m-30) REVERT: C 82 LEU cc_start: 0.6254 (mt) cc_final: 0.6013 (mt) REVERT: C 137 MET cc_start: 0.7001 (tmm) cc_final: 0.6742 (tmm) REVERT: C 143 HIS cc_start: 0.7887 (m170) cc_final: 0.7614 (m-70) REVERT: C 173 GLU cc_start: 0.6276 (tt0) cc_final: 0.5510 (tm-30) REVERT: C 211 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.5778 (mmm) REVERT: D 225 THR cc_start: 0.8217 (p) cc_final: 0.7870 (m) REVERT: B 136 ASP cc_start: 0.6584 (m-30) cc_final: 0.6329 (m-30) REVERT: B 177 ARG cc_start: 0.7347 (mmt180) cc_final: 0.5867 (mpt180) REVERT: B 236 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7258 (mt-10) REVERT: E 140 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7806 (mmm) REVERT: E 165 LEU cc_start: 0.7274 (mt) cc_final: 0.6887 (mm) REVERT: E 178 ARG cc_start: 0.8150 (mtt180) cc_final: 0.7848 (mtt180) REVERT: E 225 THR cc_start: 0.8164 (p) cc_final: 0.7881 (t) REVERT: G 236 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7220 (mt-10) REVERT: H 140 MET cc_start: 0.8296 (mmm) cc_final: 0.7886 (tpp) REVERT: H 225 THR cc_start: 0.8238 (p) cc_final: 0.7931 (m) REVERT: I 225 THR cc_start: 0.8247 (p) cc_final: 0.7916 (m) REVERT: J 178 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7809 (mtt180) REVERT: J 242 GLU cc_start: 0.7401 (tt0) cc_final: 0.7097 (mt-10) REVERT: F 140 MET cc_start: 0.8181 (mmm) cc_final: 0.7920 (mmm) REVERT: F 225 THR cc_start: 0.8254 (p) cc_final: 0.8039 (m) outliers start: 48 outliers final: 20 residues processed: 403 average time/residue: 0.5171 time to fit residues: 237.4775 Evaluate side-chains 368 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 343 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain N residue 18 MET Chi-restraints excluded: chain N residue 37 ARG Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 12 MET Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain J residue 211 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 115 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 146 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 17 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 180 GLN ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 HIS C 180 GLN E 143 HIS G 143 HIS H 143 HIS I 180 GLN J 180 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.242217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.216283 restraints weight = 15437.995| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 1.26 r_work: 0.4244 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4136 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19250 Z= 0.148 Angle : 0.551 4.987 25960 Z= 0.282 Chirality : 0.045 0.130 2970 Planarity : 0.004 0.038 3260 Dihedral : 6.554 39.295 2718 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.01 % Allowed : 12.04 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.63 (0.17), residues: 2280 helix: 0.61 (0.17), residues: 880 sheet: 0.43 (0.22), residues: 610 loop : -2.32 (0.17), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 63 TYR 0.013 0.002 TYR E 109 PHE 0.020 0.002 PHE H 244 TRP 0.005 0.001 TRP M 79 HIS 0.010 0.001 HIS Q 31 Details of bonding type rmsd covalent geometry : bond 0.00352 (19220) covalent geometry : angle 0.55118 (25960) hydrogen bonds : bond 0.04863 ( 551) hydrogen bonds : angle 4.31607 ( 1653) metal coordination : bond 0.00559 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 356 time to evaluate : 0.718 Fit side-chains REVERT: A 211 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6309 (mmm) REVERT: K 12 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6483 (pmt) REVERT: L 37 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7387 (ttp-170) REVERT: M 12 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6192 (pmt) REVERT: N 23 GLN cc_start: 0.7011 (mt0) cc_final: 0.6808 (pt0) REVERT: O 51 ASP cc_start: 0.7388 (m-30) cc_final: 0.7125 (m-30) REVERT: Q 23 GLN cc_start: 0.7256 (pt0) cc_final: 0.6875 (pm20) REVERT: Q 37 ARG cc_start: 0.7552 (ptt180) cc_final: 0.7347 (ttp-170) REVERT: S 37 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7068 (ptt180) REVERT: T 29 MET cc_start: 0.7080 (mmp) cc_final: 0.6448 (mmp) REVERT: C 77 SER cc_start: 0.6620 (OUTLIER) cc_final: 0.5825 (m) REVERT: C 82 LEU cc_start: 0.6418 (mt) cc_final: 0.6197 (mt) REVERT: B 136 ASP cc_start: 0.6462 (m-30) cc_final: 0.6255 (m-30) REVERT: B 168 LEU cc_start: 0.7960 (mt) cc_final: 0.7547 (tp) REVERT: B 211 MET cc_start: 0.6760 (mtm) cc_final: 0.6395 (mmm) REVERT: E 178 ARG cc_start: 0.8123 (mtt180) cc_final: 0.7810 (mtt180) REVERT: E 211 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6152 (mmm) REVERT: E 225 THR cc_start: 0.8142 (p) cc_final: 0.7701 (t) REVERT: H 140 MET cc_start: 0.8340 (mmm) cc_final: 0.7991 (tpp) REVERT: H 225 THR cc_start: 0.8241 (p) cc_final: 0.7943 (m) REVERT: J 128 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7251 (pp20) REVERT: J 129 MET cc_start: 0.8130 (ttm) cc_final: 0.7447 (mtt) REVERT: J 168 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7587 (mp) REVERT: J 211 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5772 (mmm) REVERT: F 140 MET cc_start: 0.8156 (mmm) cc_final: 0.7873 (tpp) REVERT: F 225 THR cc_start: 0.8126 (p) cc_final: 0.7812 (m) outliers start: 62 outliers final: 26 residues processed: 386 average time/residue: 0.5273 time to fit residues: 231.6506 Evaluate side-chains 370 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 334 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 12 MET Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 148 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS C 143 HIS D 180 GLN G 143 HIS H 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.242501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.216708 restraints weight = 15423.450| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 1.25 r_work: 0.4250 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4141 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19250 Z= 0.137 Angle : 0.524 4.989 25960 Z= 0.267 Chirality : 0.045 0.131 2970 Planarity : 0.004 0.039 3260 Dihedral : 6.180 38.152 2718 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.69 % Allowed : 12.91 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.02 (0.18), residues: 2280 helix: 1.36 (0.18), residues: 880 sheet: 0.27 (0.21), residues: 670 loop : -2.00 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 97 TYR 0.014 0.002 TYR B 109 PHE 0.022 0.002 PHE G 244 TRP 0.005 0.001 TRP M 79 HIS 0.008 0.001 HIS Q 31 Details of bonding type rmsd covalent geometry : bond 0.00326 (19220) covalent geometry : angle 0.52442 (25960) hydrogen bonds : bond 0.04384 ( 551) hydrogen bonds : angle 4.21724 ( 1653) metal coordination : bond 0.00432 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 351 time to evaluate : 0.696 Fit side-chains REVERT: A 211 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6463 (mmm) REVERT: L 23 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6844 (pm20) REVERT: L 37 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7362 (ttp-170) REVERT: M 12 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6086 (pmt) REVERT: N 12 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.6145 (pmt) REVERT: N 23 GLN cc_start: 0.7094 (mt0) cc_final: 0.6780 (pt0) REVERT: O 29 MET cc_start: 0.7103 (mmp) cc_final: 0.6561 (mmp) REVERT: O 51 ASP cc_start: 0.7375 (m-30) cc_final: 0.7119 (m-30) REVERT: R 46 GLU cc_start: 0.7671 (pt0) cc_final: 0.6926 (pt0) REVERT: S 12 MET cc_start: 0.6675 (OUTLIER) cc_final: 0.5907 (pmt) REVERT: S 37 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7123 (ptt180) REVERT: T 51 ASP cc_start: 0.7374 (m-30) cc_final: 0.7131 (m-30) REVERT: C 77 SER cc_start: 0.6808 (OUTLIER) cc_final: 0.6028 (m) REVERT: D 128 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7333 (pp20) REVERT: D 244 PHE cc_start: 0.8393 (t80) cc_final: 0.8186 (t80) REVERT: E 129 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7785 (mmt) REVERT: E 178 ARG cc_start: 0.8150 (mtt180) cc_final: 0.7871 (mtt180) REVERT: E 211 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.6284 (mmm) REVERT: E 225 THR cc_start: 0.8203 (p) cc_final: 0.7758 (t) REVERT: H 140 MET cc_start: 0.8339 (mmm) cc_final: 0.7943 (tpp) REVERT: H 225 THR cc_start: 0.8260 (p) cc_final: 0.7909 (m) REVERT: J 128 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.6994 (pp20) REVERT: J 129 MET cc_start: 0.8135 (ttm) cc_final: 0.7580 (mtt) REVERT: J 168 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7540 (mp) REVERT: J 211 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.5652 (mmm) REVERT: F 211 MET cc_start: 0.6494 (OUTLIER) cc_final: 0.6023 (mmm) REVERT: F 225 THR cc_start: 0.8143 (p) cc_final: 0.7757 (m) outliers start: 76 outliers final: 36 residues processed: 391 average time/residue: 0.5297 time to fit residues: 235.9940 Evaluate side-chains 382 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 331 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 23 GLN Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 12 MET Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 168 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 215 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4543 r_free = 0.4543 target = 0.240325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.214418 restraints weight = 15368.353| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 1.25 r_work: 0.4232 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19250 Z= 0.164 Angle : 0.563 5.480 25960 Z= 0.285 Chirality : 0.046 0.136 2970 Planarity : 0.004 0.038 3260 Dihedral : 6.396 38.807 2718 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.42 % Allowed : 12.67 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.08 (0.18), residues: 2280 helix: 1.52 (0.17), residues: 870 sheet: 0.26 (0.21), residues: 670 loop : -1.95 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 235 TYR 0.019 0.002 TYR B 109 PHE 0.024 0.002 PHE G 244 TRP 0.005 0.001 TRP M 79 HIS 0.006 0.001 HIS Q 31 Details of bonding type rmsd covalent geometry : bond 0.00394 (19220) covalent geometry : angle 0.56255 (25960) hydrogen bonds : bond 0.04712 ( 551) hydrogen bonds : angle 4.31412 ( 1653) metal coordination : bond 0.00529 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 340 time to evaluate : 0.552 Fit side-chains REVERT: A 211 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6307 (mmm) REVERT: L 3 TYR cc_start: 0.7760 (m-80) cc_final: 0.7504 (m-80) REVERT: L 23 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6915 (pm20) REVERT: M 12 MET cc_start: 0.6871 (OUTLIER) cc_final: 0.6170 (pmt) REVERT: M 46 GLU cc_start: 0.7555 (pt0) cc_final: 0.7142 (pt0) REVERT: N 12 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.5991 (pmt) REVERT: N 23 GLN cc_start: 0.6976 (mt0) cc_final: 0.6774 (pt0) REVERT: N 37 ARG cc_start: 0.7514 (ttp-170) cc_final: 0.7222 (ttp-170) REVERT: P 37 ARG cc_start: 0.7517 (ptt180) cc_final: 0.7222 (ttp-170) REVERT: Q 3 TYR cc_start: 0.7711 (m-80) cc_final: 0.7486 (m-80) REVERT: Q 23 GLN cc_start: 0.7268 (pt0) cc_final: 0.6839 (pm20) REVERT: R 46 GLU cc_start: 0.7646 (pt0) cc_final: 0.7029 (pt0) REVERT: S 12 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.5775 (pmt) REVERT: S 37 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7207 (ptt180) REVERT: C 77 SER cc_start: 0.6570 (OUTLIER) cc_final: 0.6104 (m) REVERT: D 128 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7304 (pp20) REVERT: D 211 MET cc_start: 0.6758 (mtm) cc_final: 0.6312 (mmm) REVERT: E 128 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.6882 (pp20) REVERT: E 129 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7374 (mmt) REVERT: E 168 LEU cc_start: 0.7824 (mt) cc_final: 0.7346 (tp) REVERT: E 178 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7863 (mtt180) REVERT: E 211 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6366 (mmm) REVERT: E 225 THR cc_start: 0.8151 (p) cc_final: 0.7666 (t) REVERT: H 140 MET cc_start: 0.8386 (mmm) cc_final: 0.8068 (tpp) REVERT: H 211 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6347 (mmm) REVERT: I 211 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.5516 (mmm) REVERT: J 128 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.6955 (pp20) REVERT: J 129 MET cc_start: 0.8195 (ttm) cc_final: 0.7796 (mtt) REVERT: J 168 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7534 (mp) REVERT: J 211 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.5990 (mmm) REVERT: F 211 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6274 (mmm) outliers start: 91 outliers final: 45 residues processed: 382 average time/residue: 0.5159 time to fit residues: 225.2794 Evaluate side-chains 388 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 326 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 23 GLN Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 12 MET Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 211 MET Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 198 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 199 optimal weight: 0.2980 chunk 19 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 214 optimal weight: 0.0970 chunk 50 optimal weight: 10.0000 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4594 r_free = 0.4594 target = 0.245850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.220577 restraints weight = 15318.640| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 1.25 r_work: 0.4294 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4187 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19250 Z= 0.094 Angle : 0.458 4.995 25960 Z= 0.235 Chirality : 0.042 0.125 2970 Planarity : 0.003 0.038 3260 Dihedral : 5.470 33.982 2718 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.62 % Allowed : 14.37 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.75 (0.18), residues: 2280 helix: 2.03 (0.18), residues: 890 sheet: 1.09 (0.24), residues: 560 loop : -1.74 (0.17), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 97 TYR 0.011 0.001 TYR B 109 PHE 0.023 0.002 PHE E 244 TRP 0.006 0.001 TRP L 79 HIS 0.006 0.001 HIS Q 31 Details of bonding type rmsd covalent geometry : bond 0.00214 (19220) covalent geometry : angle 0.45761 (25960) hydrogen bonds : bond 0.03667 ( 551) hydrogen bonds : angle 4.00655 ( 1653) metal coordination : bond 0.00309 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 352 time to evaluate : 0.620 Fit side-chains REVERT: A 211 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.6070 (mmm) REVERT: L 18 MET cc_start: 0.8090 (mmt) cc_final: 0.7825 (mmt) REVERT: L 23 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.7052 (pm20) REVERT: L 37 ARG cc_start: 0.7694 (ttp-170) cc_final: 0.7232 (ttp-170) REVERT: M 46 GLU cc_start: 0.7505 (pt0) cc_final: 0.6985 (pt0) REVERT: N 18 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.6693 (mmt) REVERT: N 23 GLN cc_start: 0.6965 (mt0) cc_final: 0.6756 (pt0) REVERT: N 37 ARG cc_start: 0.7424 (ttp-170) cc_final: 0.7078 (ttp-170) REVERT: O 37 ARG cc_start: 0.7616 (ttp-170) cc_final: 0.7412 (ttp-170) REVERT: O 51 ASP cc_start: 0.7302 (m-30) cc_final: 0.7067 (m-30) REVERT: Q 3 TYR cc_start: 0.7662 (m-80) cc_final: 0.7423 (m-80) REVERT: Q 23 GLN cc_start: 0.7130 (pt0) cc_final: 0.6842 (pm20) REVERT: Q 46 GLU cc_start: 0.7783 (pt0) cc_final: 0.7477 (pt0) REVERT: R 46 GLU cc_start: 0.7679 (pt0) cc_final: 0.7148 (pt0) REVERT: T 51 ASP cc_start: 0.7342 (m-30) cc_final: 0.7115 (m-30) REVERT: C 77 SER cc_start: 0.6523 (OUTLIER) cc_final: 0.6060 (m) REVERT: C 211 MET cc_start: 0.6900 (mtm) cc_final: 0.6411 (mmm) REVERT: D 211 MET cc_start: 0.6487 (mtm) cc_final: 0.5982 (mmm) REVERT: B 230 MET cc_start: 0.8053 (mmt) cc_final: 0.7815 (mmt) REVERT: E 109 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.7226 (p90) REVERT: E 178 ARG cc_start: 0.8071 (mtt180) cc_final: 0.7738 (mtt180) REVERT: E 211 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.6087 (mmm) REVERT: E 225 THR cc_start: 0.8058 (p) cc_final: 0.7609 (t) REVERT: G 137 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6924 (tmm) REVERT: G 211 MET cc_start: 0.5887 (OUTLIER) cc_final: 0.5624 (mtm) REVERT: H 140 MET cc_start: 0.8384 (mmm) cc_final: 0.8015 (tpp) REVERT: H 211 MET cc_start: 0.6996 (mtm) cc_final: 0.6409 (mmm) REVERT: H 225 THR cc_start: 0.8219 (p) cc_final: 0.7850 (m) REVERT: J 168 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7588 (mp) REVERT: J 211 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.5961 (mmm) REVERT: F 211 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6131 (mmm) outliers start: 54 outliers final: 25 residues processed: 383 average time/residue: 0.5088 time to fit residues: 222.8396 Evaluate side-chains 363 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 327 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 23 GLN Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 18 MET Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 211 MET Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 3.9990 chunk 217 optimal weight: 0.0000 chunk 58 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.0050 chunk 6 optimal weight: 0.5980 overall best weight: 0.9000 ------------------------------------------------------------------------------- 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 = 0.4585 r_free = 0.4585 target = 0.244728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.218932 restraints weight = 15467.525| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 1.26 r_work: 0.4271 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4162 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19250 Z= 0.112 Angle : 0.481 5.025 25960 Z= 0.245 Chirality : 0.043 0.130 2970 Planarity : 0.003 0.036 3260 Dihedral : 5.418 32.973 2718 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.86 % Allowed : 14.66 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.66 (0.18), residues: 2280 helix: 2.05 (0.18), residues: 890 sheet: 0.45 (0.22), residues: 670 loop : -1.70 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 178 TYR 0.013 0.001 TYR B 109 PHE 0.020 0.002 PHE E 244 TRP 0.004 0.001 TRP J 96 HIS 0.005 0.001 HIS Q 31 Details of bonding type rmsd covalent geometry : bond 0.00265 (19220) covalent geometry : angle 0.48097 (25960) hydrogen bonds : bond 0.03959 ( 551) hydrogen bonds : angle 4.03171 ( 1653) metal coordination : bond 0.00343 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 349 time to evaluate : 0.692 Fit side-chains REVERT: A 168 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7557 (mp) REVERT: A 211 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6161 (mmm) REVERT: L 23 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.7017 (pm20) REVERT: L 37 ARG cc_start: 0.7655 (ttp-170) cc_final: 0.7353 (ttp-170) REVERT: L 65 PHE cc_start: 0.8231 (m-80) cc_final: 0.7850 (m-10) REVERT: M 46 GLU cc_start: 0.7526 (pt0) cc_final: 0.6990 (pt0) REVERT: N 37 ARG cc_start: 0.7434 (ttp-170) cc_final: 0.7039 (ttp-170) REVERT: O 12 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6521 (ptp) REVERT: O 51 ASP cc_start: 0.7287 (m-30) cc_final: 0.7052 (m-30) REVERT: Q 3 TYR cc_start: 0.7688 (m-80) cc_final: 0.7445 (m-80) REVERT: Q 23 GLN cc_start: 0.7169 (pt0) cc_final: 0.6836 (pm20) REVERT: R 46 GLU cc_start: 0.7667 (pt0) cc_final: 0.7158 (pt0) REVERT: S 37 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7002 (ttp-170) REVERT: T 51 ASP cc_start: 0.7320 (m-30) cc_final: 0.7097 (m-30) REVERT: C 77 SER cc_start: 0.6624 (OUTLIER) cc_final: 0.6160 (m) REVERT: C 183 GLU cc_start: 0.6658 (mt-10) cc_final: 0.6351 (mt-10) REVERT: D 211 MET cc_start: 0.6601 (mtm) cc_final: 0.6110 (mmm) REVERT: B 230 MET cc_start: 0.8084 (mmt) cc_final: 0.7797 (mmt) REVERT: B 242 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6928 (mt-10) REVERT: E 97 ARG cc_start: 0.6933 (mtm-85) cc_final: 0.6574 (mtm180) REVERT: E 109 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.7207 (p90) REVERT: E 128 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.6912 (pp20) REVERT: E 178 ARG cc_start: 0.8095 (mtt180) cc_final: 0.7792 (mtt180) REVERT: E 211 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6202 (mmm) REVERT: E 225 THR cc_start: 0.8070 (p) cc_final: 0.7600 (t) REVERT: G 137 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6928 (tmm) REVERT: H 140 MET cc_start: 0.8386 (mmm) cc_final: 0.7999 (tpp) REVERT: H 211 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6238 (mmm) REVERT: H 225 THR cc_start: 0.8226 (p) cc_final: 0.7865 (m) REVERT: J 168 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7551 (mp) REVERT: J 211 MET cc_start: 0.6695 (OUTLIER) cc_final: 0.6017 (mmm) REVERT: F 211 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6169 (mmm) outliers start: 59 outliers final: 34 residues processed: 388 average time/residue: 0.5175 time to fit residues: 229.8206 Evaluate side-chains 380 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 331 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 23 GLN Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 178 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 94 optimal weight: 0.0050 chunk 146 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.245695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.220180 restraints weight = 15360.210| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 1.25 r_work: 0.4282 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4174 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19250 Z= 0.102 Angle : 0.466 5.024 25960 Z= 0.238 Chirality : 0.043 0.128 2970 Planarity : 0.003 0.036 3260 Dihedral : 5.199 31.069 2718 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.77 % Allowed : 15.29 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.01 (0.18), residues: 2280 helix: 2.25 (0.18), residues: 890 sheet: 1.19 (0.24), residues: 560 loop : -1.58 (0.18), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 97 TYR 0.012 0.001 TYR B 109 PHE 0.022 0.002 PHE E 244 TRP 0.005 0.001 TRP L 79 HIS 0.006 0.001 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00239 (19220) covalent geometry : angle 0.46564 (25960) hydrogen bonds : bond 0.03770 ( 551) hydrogen bonds : angle 3.99743 ( 1653) metal coordination : bond 0.00285 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 333 time to evaluate : 0.463 Fit side-chains REVERT: A 168 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7545 (mp) REVERT: A 211 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6053 (mmm) REVERT: L 23 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: L 37 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.7182 (ttp-170) REVERT: M 46 GLU cc_start: 0.7569 (pt0) cc_final: 0.7041 (pt0) REVERT: O 12 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6525 (ptp) REVERT: O 51 ASP cc_start: 0.7292 (m-30) cc_final: 0.7068 (m-30) REVERT: Q 3 TYR cc_start: 0.7697 (m-80) cc_final: 0.7453 (m-80) REVERT: Q 23 GLN cc_start: 0.7285 (pt0) cc_final: 0.7024 (pm20) REVERT: R 46 GLU cc_start: 0.7714 (pt0) cc_final: 0.7205 (pt0) REVERT: S 37 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7127 (ptt180) REVERT: T 51 ASP cc_start: 0.7333 (m-30) cc_final: 0.7113 (m-30) REVERT: C 77 SER cc_start: 0.6624 (OUTLIER) cc_final: 0.6156 (m) REVERT: C 129 MET cc_start: 0.7945 (ttm) cc_final: 0.7653 (mmt) REVERT: D 128 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7426 (pp20) REVERT: D 211 MET cc_start: 0.6390 (mtm) cc_final: 0.6037 (mmm) REVERT: B 242 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6935 (mt-10) REVERT: E 109 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.7259 (p90) REVERT: E 128 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.6936 (pp20) REVERT: E 178 ARG cc_start: 0.8106 (mtt180) cc_final: 0.7843 (mtt180) REVERT: E 211 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.6062 (mmm) REVERT: E 225 THR cc_start: 0.7999 (p) cc_final: 0.7637 (m) REVERT: G 137 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6918 (tmm) REVERT: G 242 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6961 (mt-10) REVERT: H 140 MET cc_start: 0.8386 (mmm) cc_final: 0.8010 (tpp) REVERT: H 211 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.6188 (mmm) REVERT: J 128 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.6914 (pp20) REVERT: J 129 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7322 (mmt) REVERT: J 149 VAL cc_start: 0.8297 (m) cc_final: 0.8076 (m) REVERT: J 168 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7583 (mp) REVERT: J 211 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6191 (mmm) REVERT: F 211 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.6110 (mmm) outliers start: 57 outliers final: 32 residues processed: 372 average time/residue: 0.5084 time to fit residues: 216.5880 Evaluate side-chains 377 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 326 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 23 GLN Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 220 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4593 r_free = 0.4593 target = 0.245634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.219987 restraints weight = 15277.668| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 1.25 r_work: 0.4289 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4181 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19250 Z= 0.106 Angle : 0.469 5.010 25960 Z= 0.240 Chirality : 0.043 0.134 2970 Planarity : 0.003 0.035 3260 Dihedral : 5.141 30.597 2718 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.72 % Allowed : 15.39 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.10 (0.18), residues: 2280 helix: 2.31 (0.18), residues: 890 sheet: 1.24 (0.24), residues: 560 loop : -1.52 (0.18), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 178 TYR 0.012 0.001 TYR B 109 PHE 0.024 0.002 PHE G 244 TRP 0.005 0.001 TRP K 79 HIS 0.007 0.001 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00251 (19220) covalent geometry : angle 0.46884 (25960) hydrogen bonds : bond 0.03832 ( 551) hydrogen bonds : angle 4.00595 ( 1653) metal coordination : bond 0.00302 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 340 time to evaluate : 0.621 Fit side-chains REVERT: A 168 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7543 (mp) REVERT: A 211 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6059 (mmm) REVERT: L 23 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: L 37 ARG cc_start: 0.7574 (ttp-170) cc_final: 0.7264 (ttp-170) REVERT: L 46 GLU cc_start: 0.7442 (pt0) cc_final: 0.7115 (pt0) REVERT: M 46 GLU cc_start: 0.7673 (pt0) cc_final: 0.7168 (pt0) REVERT: O 12 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6475 (ptp) REVERT: O 51 ASP cc_start: 0.7284 (m-30) cc_final: 0.7058 (m-30) REVERT: Q 3 TYR cc_start: 0.7693 (m-80) cc_final: 0.7435 (m-80) REVERT: Q 23 GLN cc_start: 0.7303 (pt0) cc_final: 0.7048 (pm20) REVERT: R 46 GLU cc_start: 0.7694 (pt0) cc_final: 0.7140 (pt0) REVERT: S 37 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7151 (ptt180) REVERT: T 37 ARG cc_start: 0.7473 (ttp-170) cc_final: 0.7125 (ttp-170) REVERT: T 51 ASP cc_start: 0.7331 (m-30) cc_final: 0.7107 (m-30) REVERT: C 77 SER cc_start: 0.6589 (OUTLIER) cc_final: 0.6119 (m) REVERT: C 129 MET cc_start: 0.7931 (ttm) cc_final: 0.7626 (mmt) REVERT: C 140 MET cc_start: 0.7840 (mmm) cc_final: 0.7577 (tpp) REVERT: C 183 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6440 (mt-10) REVERT: D 211 MET cc_start: 0.6392 (mtm) cc_final: 0.6051 (mmm) REVERT: B 242 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6848 (mt-10) REVERT: E 109 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.7207 (p90) REVERT: E 128 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7005 (pp20) REVERT: E 178 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7759 (mtt180) REVERT: E 211 MET cc_start: 0.6573 (OUTLIER) cc_final: 0.6021 (mmm) REVERT: E 225 THR cc_start: 0.7989 (p) cc_final: 0.7654 (m) REVERT: G 242 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6973 (mt-10) REVERT: H 140 MET cc_start: 0.8387 (mmm) cc_final: 0.8021 (tpp) REVERT: H 211 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6306 (mmm) REVERT: J 128 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.6861 (pp20) REVERT: J 129 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7317 (mmt) REVERT: J 149 VAL cc_start: 0.8282 (m) cc_final: 0.8074 (m) REVERT: J 168 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7545 (mp) REVERT: J 211 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.5992 (mmm) REVERT: F 211 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6047 (mmm) outliers start: 56 outliers final: 33 residues processed: 378 average time/residue: 0.5156 time to fit residues: 222.8578 Evaluate side-chains 382 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 332 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 23 GLN Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 197 optimal weight: 2.9990 chunk 182 optimal weight: 0.0970 chunk 69 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.240169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.214072 restraints weight = 15582.087| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 1.26 r_work: 0.4227 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19250 Z= 0.162 Angle : 0.555 9.956 25960 Z= 0.279 Chirality : 0.046 0.137 2970 Planarity : 0.004 0.034 3260 Dihedral : 5.853 35.197 2718 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.48 % Allowed : 15.68 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.62 (0.18), residues: 2280 helix: 2.02 (0.17), residues: 880 sheet: 0.49 (0.22), residues: 670 loop : -1.73 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 241 TYR 0.020 0.002 TYR J 109 PHE 0.028 0.003 PHE E 244 TRP 0.006 0.001 TRP M 79 HIS 0.006 0.001 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00395 (19220) covalent geometry : angle 0.55473 (25960) hydrogen bonds : bond 0.04571 ( 551) hydrogen bonds : angle 4.25406 ( 1653) metal coordination : bond 0.00440 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 330 time to evaluate : 0.657 Fit side-chains REVERT: A 140 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7511 (tpp) REVERT: A 168 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7583 (mp) REVERT: A 211 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6381 (mmm) REVERT: L 23 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7114 (pm20) REVERT: M 46 GLU cc_start: 0.7665 (pt0) cc_final: 0.7113 (pt0) REVERT: O 12 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6518 (ptp) REVERT: Q 3 TYR cc_start: 0.7742 (m-80) cc_final: 0.7471 (m-80) REVERT: Q 23 GLN cc_start: 0.7402 (pt0) cc_final: 0.7041 (pm20) REVERT: R 46 GLU cc_start: 0.7601 (pt0) cc_final: 0.7131 (pt0) REVERT: S 37 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7162 (ptt180) REVERT: T 51 ASP cc_start: 0.7394 (m-30) cc_final: 0.7149 (m-30) REVERT: C 77 SER cc_start: 0.6711 (OUTLIER) cc_final: 0.6231 (m) REVERT: C 140 MET cc_start: 0.7975 (mmm) cc_final: 0.7673 (tpp) REVERT: C 183 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6509 (mt-10) REVERT: C 211 MET cc_start: 0.6893 (mtm) cc_final: 0.6204 (mmm) REVERT: D 211 MET cc_start: 0.6790 (mtm) cc_final: 0.6402 (mmm) REVERT: E 128 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7027 (pp20) REVERT: E 178 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7877 (mtt180) REVERT: E 211 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6316 (mmm) REVERT: G 140 MET cc_start: 0.7984 (tpp) cc_final: 0.7772 (mmm) REVERT: H 140 MET cc_start: 0.8440 (mmm) cc_final: 0.8100 (tpp) REVERT: H 211 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6404 (mmm) REVERT: I 211 MET cc_start: 0.6364 (mtp) cc_final: 0.5803 (mmm) REVERT: J 128 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.6847 (pp20) REVERT: J 129 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7414 (mmt) REVERT: J 168 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7558 (mp) REVERT: J 211 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6460 (mmm) REVERT: F 211 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6415 (mmm) outliers start: 51 outliers final: 35 residues processed: 365 average time/residue: 0.5194 time to fit residues: 216.7733 Evaluate side-chains 374 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 324 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 23 GLN Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 41 optimal weight: 7.9990 chunk 133 optimal weight: 0.0970 chunk 117 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4581 r_free = 0.4581 target = 0.245419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.219460 restraints weight = 15699.308| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 1.28 r_work: 0.4282 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4180 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19250 Z= 0.096 Angle : 0.460 6.893 25960 Z= 0.235 Chirality : 0.042 0.133 2970 Planarity : 0.003 0.035 3260 Dihedral : 5.173 31.533 2718 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.38 % Allowed : 15.87 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.17 (0.18), residues: 2280 helix: 2.37 (0.18), residues: 890 sheet: 1.25 (0.24), residues: 560 loop : -1.44 (0.18), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 249 TYR 0.012 0.001 TYR J 175 PHE 0.023 0.002 PHE B 244 TRP 0.008 0.001 TRP S 79 HIS 0.005 0.001 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00222 (19220) covalent geometry : angle 0.45973 (25960) hydrogen bonds : bond 0.03689 ( 551) hydrogen bonds : angle 4.03023 ( 1653) metal coordination : bond 0.00302 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6356.90 seconds wall clock time: 108 minutes 49.46 seconds (6529.46 seconds total)