Starting phenix.real_space_refine on Mon Sep 14 21:04:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6z85_11114/09_2026/6z85_11114.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z85_11114/09_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_11114/09_2026/6z85_11114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z85_11114/09_2026/6z85_11114.map" model { file = "/net/cci-nas-00/data/ceres_data/6z85_11114/09_2026/6z85_11114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z85_11114/09_2026/6z85_11114.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6z85_11114/09_2026/6z85_11114.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6z85_11114/09_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 2.17, per 1000 atoms: 0.11 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: 1.62 Conformation dependent library (CDL) restraints added in 781.2 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: 0.42 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: 2.91 Time building geometry restraints manager: 2.11 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: 11098 14.52 - 29.03: 452 29.03 - 43.54: 60 43.54 - 58.06: 30 58.06 - 72.57: 10 Dihedral angle restraints: 11650 sinusoidal: 4850 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 11647 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: 0.07 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.010 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 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 : 9.336 72.575 7250 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/Z covalent geometry : bond 0.00905 / 0.37 (19220) covalent geometry : angle 1.04802 / 0.59 (25960) hydrogen bonds : bond 0.34261 / 21.99 ( 551) hydrogen bonds : angle 10.28941 / 6.97 ( 1653) metal coordination : bond 0.35286 / 20.75 ( 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 : 0.847 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: 0.5839 time to fit residues: 328.2548 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 : 0.718 ------------------------------------------------------------------------------- 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... ** 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 180 GLN F 143 HIS F 180 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.244358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.220384 restraints weight = 15552.247| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 1.13 r_work: 0.4227 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4117 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19250 Z= 0.136 Angle : 0.548 6.297 25960 Z= 0.284 Chirality : 0.044 0.127 2970 Planarity : 0.005 0.044 3260 Dihedral : 5.293 27.700 2620 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.38 % Allowed : 10.05 % 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: -1.96 (0.16), residues: 2280 helix: -1.11 (0.16), residues: 890 sheet: -0.20 (0.20), residues: 670 loop : -2.42 (0.18), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 97 TYR 0.011 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/Z covalent geometry : bond 0.00316 / 0.14 (19220) covalent geometry : angle 0.54811 / 0.28 (25960) hydrogen bonds : bond 0.04902 / 3.17 ( 551) hydrogen bonds : angle 4.67223 / 3.16 ( 1653) metal coordination : bond 0.00637 / 0.36 ( 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 426 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 377 time to evaluate : 0.721 Fit side-chains REVERT: A 211 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6467 (OUTLIER) REVERT: K 54 ARG cc_start: 0.6527 (ttp-110) cc_final: 0.6157 (ttm110) REVERT: L 37 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7328 (ttp-170) REVERT: N 18 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.6670 (mmt) REVERT: N 23 GLN cc_start: 0.7028 (mt0) cc_final: 0.6809 (pt0) REVERT: N 37 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.6974 (ptt90) REVERT: O 29 MET cc_start: 0.6995 (mmp) cc_final: 0.6410 (mmp) REVERT: C 82 LEU cc_start: 0.6402 (mt) cc_final: 0.6137 (mt) REVERT: C 137 MET cc_start: 0.7015 (tmm) cc_final: 0.6750 (tmm) REVERT: C 143 HIS cc_start: 0.7825 (m170) cc_final: 0.7532 (m-70) REVERT: C 173 GLU cc_start: 0.6275 (tt0) cc_final: 0.5518 (tm-30) REVERT: C 211 MET cc_start: 0.6566 (OUTLIER) cc_final: 0.5910 (mmm) REVERT: D 225 THR cc_start: 0.8315 (p) cc_final: 0.7965 (m) REVERT: B 136 ASP cc_start: 0.6555 (m-30) cc_final: 0.6308 (m-30) REVERT: B 177 ARG cc_start: 0.7333 (mmt180) cc_final: 0.5879 (mpt180) REVERT: B 236 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7273 (mt-10) REVERT: E 140 MET cc_start: 0.8169 (mmm) cc_final: 0.7600 (mmm) REVERT: E 165 LEU cc_start: 0.7279 (mt) cc_final: 0.6900 (mm) REVERT: E 225 THR cc_start: 0.8048 (p) cc_final: 0.7775 (t) REVERT: G 236 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7235 (mt-10) REVERT: H 140 MET cc_start: 0.8314 (mmm) cc_final: 0.7840 (tpp) REVERT: H 225 THR cc_start: 0.8251 (p) cc_final: 0.7941 (m) REVERT: I 225 THR cc_start: 0.8347 (p) cc_final: 0.8027 (m) REVERT: I 242 GLU cc_start: 0.7607 (tt0) cc_final: 0.7390 (mt-10) REVERT: J 178 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7784 (mtt180) REVERT: J 242 GLU cc_start: 0.7360 (tt0) cc_final: 0.7016 (mt-10) REVERT: F 140 MET cc_start: 0.8204 (mmm) cc_final: 0.7972 (mmm) REVERT: F 225 THR cc_start: 0.8276 (p) cc_final: 0.8038 (m) outliers start: 49 outliers final: 21 residues processed: 399 average time/residue: 0.5152 time to fit residues: 235.4451 Evaluate side-chains 369 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 344 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 19 VAL 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 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: 0.0970 chunk 31 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS A 180 GLN C 143 HIS C 180 GLN E 143 HIS G 143 HIS H 143 HIS I 180 GLN J 143 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.240971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.214858 restraints weight = 15434.302| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 1.25 r_work: 0.4233 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19250 Z= 0.164 Angle : 0.575 5.734 25960 Z= 0.293 Chirality : 0.046 0.138 2970 Planarity : 0.004 0.039 3260 Dihedral : 5.207 27.765 2618 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.25 % Allowed : 12.14 % Favored : 84.61 % 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: -0.77 (0.17), residues: 2280 helix: 0.47 (0.17), residues: 880 sheet: 0.39 (0.22), residues: 610 loop : -2.38 (0.17), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 63 TYR 0.014 0.002 TYR B 109 PHE 0.020 0.002 PHE A 148 TRP 0.005 0.001 TRP M 79 HIS 0.009 0.001 HIS L 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (19220) covalent geometry : angle 0.57480 / 0.29 (25960) hydrogen bonds : bond 0.05071 / 3.31 ( 551) hydrogen bonds : angle 4.38904 / 2.97 ( 1653) metal coordination : bond 0.00579 / 0.34 ( 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 426 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 359 time to evaluate : 0.700 Fit side-chains REVERT: A 183 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6541 (mt-10) REVERT: A 211 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6366 (mmm) REVERT: K 12 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6436 (pmt) REVERT: L 37 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7399 (ttp-170) REVERT: N 18 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.6857 (mmt) REVERT: N 23 GLN cc_start: 0.6973 (mt0) cc_final: 0.6742 (pt0) REVERT: Q 23 GLN cc_start: 0.7319 (pt0) cc_final: 0.6861 (pm20) REVERT: Q 37 ARG cc_start: 0.7581 (ptt180) cc_final: 0.7364 (ttp-170) REVERT: S 37 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7080 (ptt180) REVERT: T 29 MET cc_start: 0.7005 (mmp) cc_final: 0.6391 (mmp) REVERT: C 77 SER cc_start: 0.6603 (OUTLIER) cc_final: 0.5827 (m) REVERT: C 82 LEU cc_start: 0.6418 (mt) cc_final: 0.6209 (mt) REVERT: C 211 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.5994 (mmm) REVERT: B 136 ASP cc_start: 0.6408 (m-30) cc_final: 0.6181 (m-30) REVERT: B 168 LEU cc_start: 0.7984 (mt) cc_final: 0.7608 (tp) REVERT: B 211 MET cc_start: 0.6900 (mtm) cc_final: 0.6628 (mmm) REVERT: E 178 ARG cc_start: 0.8133 (mtt180) cc_final: 0.7817 (mtt180) REVERT: E 211 MET cc_start: 0.6684 (OUTLIER) cc_final: 0.6194 (mmm) REVERT: E 225 THR cc_start: 0.8149 (p) cc_final: 0.7702 (t) REVERT: H 140 MET cc_start: 0.8351 (mmm) cc_final: 0.8041 (tpp) REVERT: H 225 THR cc_start: 0.8273 (p) cc_final: 0.7952 (m) REVERT: I 140 MET cc_start: 0.8224 (mmm) cc_final: 0.7992 (mmm) REVERT: J 128 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.6951 (pp20) REVERT: J 129 MET cc_start: 0.8166 (ttm) cc_final: 0.7568 (mtt) REVERT: J 168 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7601 (mp) REVERT: J 211 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.5839 (mmm) REVERT: F 140 MET cc_start: 0.8142 (mmm) cc_final: 0.7846 (tpp) REVERT: F 225 THR cc_start: 0.8157 (p) cc_final: 0.7825 (m) outliers start: 67 outliers final: 24 residues processed: 387 average time/residue: 0.5016 time to fit residues: 223.0159 Evaluate side-chains 370 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 335 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 12 MET Chi-restraints excluded: chain K residue 19 VAL 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 19 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain N residue 18 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 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 211 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 149 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 191 VAL 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: 0.9980 chunk 139 optimal weight: 0.7980 chunk 172 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 212 optimal weight: 0.0870 chunk 39 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS C 143 HIS D 180 GLN G 143 HIS H 143 HIS H 180 GLN J 180 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.240838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.216868 restraints weight = 15371.870| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 1.21 r_work: 0.4257 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4153 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19250 Z= 0.158 Angle : 0.557 5.038 25960 Z= 0.283 Chirality : 0.046 0.133 2970 Planarity : 0.004 0.039 3260 Dihedral : 5.052 26.665 2618 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.98 % Allowed : 12.52 % Favored : 83.50 % 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: -0.22 (0.17), residues: 2280 helix: 1.20 (0.17), residues: 870 sheet: 0.18 (0.21), residues: 670 loop : -2.09 (0.18), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 235 TYR 0.017 0.002 TYR B 109 PHE 0.022 0.002 PHE E 244 TRP 0.005 0.001 TRP R 79 HIS 0.008 0.001 HIS Q 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (19220) covalent geometry : angle 0.55723 / 0.28 (25960) hydrogen bonds : bond 0.04711 / 3.07 ( 551) hydrogen bonds : angle 4.32762 / 2.92 ( 1653) metal coordination : bond 0.00509 / 0.29 ( 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 436 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 354 time to evaluate : 0.659 Fit side-chains REVERT: A 211 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6310 (mmm) REVERT: K 37 ARG cc_start: 0.7301 (ptt180) cc_final: 0.7053 (ttp-170) REVERT: L 37 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7327 (ttp-170) REVERT: N 12 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.6025 (pmt) REVERT: N 23 GLN cc_start: 0.7066 (mt0) cc_final: 0.6830 (pt0) REVERT: O 29 MET cc_start: 0.7214 (mmp) cc_final: 0.6610 (mmp) REVERT: O 37 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7391 (ptt180) REVERT: O 51 ASP cc_start: 0.7375 (m-30) cc_final: 0.7103 (m-30) REVERT: P 12 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6425 (pmt) REVERT: R 46 GLU cc_start: 0.7634 (pt0) cc_final: 0.6950 (pt0) REVERT: S 12 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.5805 (pmt) REVERT: S 37 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7129 (ptt180) REVERT: T 29 MET cc_start: 0.7226 (mmp) cc_final: 0.6560 (mmp) REVERT: C 77 SER cc_start: 0.7001 (OUTLIER) cc_final: 0.6204 (m) REVERT: C 211 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6145 (mmm) REVERT: D 211 MET cc_start: 0.6741 (mtm) cc_final: 0.6282 (mmm) REVERT: E 128 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7240 (pp20) REVERT: E 129 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7380 (mmt) REVERT: E 178 ARG cc_start: 0.8141 (mtt180) cc_final: 0.7785 (mtt180) REVERT: E 211 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.6303 (mmm) REVERT: E 225 THR cc_start: 0.8181 (p) cc_final: 0.7737 (t) REVERT: H 140 MET cc_start: 0.8399 (mmm) cc_final: 0.8019 (tpp) REVERT: H 211 MET cc_start: 0.6871 (OUTLIER) cc_final: 0.6156 (mmm) REVERT: H 225 THR cc_start: 0.8380 (p) cc_final: 0.7950 (m) REVERT: I 140 MET cc_start: 0.8246 (mmm) cc_final: 0.7975 (mmm) REVERT: I 211 MET cc_start: 0.5875 (OUTLIER) cc_final: 0.5377 (mmm) REVERT: J 128 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.6902 (pp20) REVERT: J 129 MET cc_start: 0.8172 (ttm) cc_final: 0.7790 (mtt) REVERT: J 168 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7664 (mp) REVERT: J 211 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.5957 (mmm) REVERT: F 211 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6221 (mmm) outliers start: 82 outliers final: 39 residues processed: 394 average time/residue: 0.5281 time to fit residues: 238.6783 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 : 0.705 ------------------------------------------------------------------------------- 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 51 ASP Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 76 THR 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 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 37 ARG 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 12 MET 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 211 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 191 VAL 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 151 LYS Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 149 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 168 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 215 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.239113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.212665 restraints weight = 15723.249| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 1.28 r_work: 0.4207 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4105 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3148 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= 0.155 Angle : 0.551 5.042 25960 Z= 0.280 Chirality : 0.045 0.133 2970 Planarity : 0.004 0.038 3260 Dihedral : 4.989 25.986 2618 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.17 % Allowed : 12.77 % Favored : 83.06 % 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: 0.01 (0.18), residues: 2280 helix: 1.47 (0.17), residues: 870 sheet: 0.19 (0.21), residues: 670 loop : -1.96 (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 0.022 0.002 PHE E 244 TRP 0.005 0.001 TRP R 79 HIS 0.006 0.001 HIS Q 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (19220) covalent geometry : angle 0.55074 / 0.28 (25960) hydrogen bonds : bond 0.04625 / 3.01 ( 551) hydrogen bonds : angle 4.30478 / 2.90 ( 1653) metal coordination : bond 0.00473 / 0.27 ( 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 430 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 344 time to evaluate : 0.713 Fit side-chains REVERT: A 211 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6430 (mmm) REVERT: K 37 ARG cc_start: 0.7349 (ptt180) cc_final: 0.7085 (ttp-170) REVERT: L 3 TYR cc_start: 0.7790 (m-80) cc_final: 0.7517 (m-80) REVERT: L 23 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6906 (pm20) REVERT: N 12 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.6034 (pmt) REVERT: N 23 GLN cc_start: 0.7064 (mt0) cc_final: 0.6849 (pt0) REVERT: N 37 ARG cc_start: 0.7460 (ttp-170) cc_final: 0.7171 (ttp-170) REVERT: P 12 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6434 (pmt) REVERT: P 29 MET cc_start: 0.7234 (mmp) cc_final: 0.6889 (mmp) REVERT: Q 3 TYR cc_start: 0.7733 (m-80) cc_final: 0.7477 (m-80) REVERT: Q 23 GLN cc_start: 0.7327 (pt0) cc_final: 0.6970 (pm20) REVERT: R 46 GLU cc_start: 0.7596 (pt0) cc_final: 0.6963 (pt0) REVERT: S 12 MET cc_start: 0.6590 (OUTLIER) cc_final: 0.5830 (pmt) REVERT: S 37 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7222 (ptt180) REVERT: C 77 SER cc_start: 0.6555 (OUTLIER) cc_final: 0.6066 (m) REVERT: C 211 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6289 (mmm) REVERT: D 128 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7225 (pp20) REVERT: D 211 MET cc_start: 0.6757 (mtm) cc_final: 0.6382 (mmm) REVERT: E 128 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7118 (pp20) REVERT: E 129 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7129 (mmt) REVERT: E 178 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7869 (mtt180) REVERT: E 211 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6224 (mmm) REVERT: E 225 THR cc_start: 0.8147 (p) cc_final: 0.7682 (t) REVERT: H 129 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7729 (mtt) REVERT: H 140 MET cc_start: 0.8341 (mmm) cc_final: 0.8018 (tpp) REVERT: H 211 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6423 (mmm) REVERT: I 140 MET cc_start: 0.8349 (mmm) cc_final: 0.8112 (tpp) REVERT: I 211 MET cc_start: 0.5835 (OUTLIER) cc_final: 0.5432 (mmm) REVERT: J 128 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.6887 (pp20) REVERT: J 168 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7596 (mp) REVERT: J 211 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.6181 (mmm) REVERT: F 211 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6242 (mmm) outliers start: 86 outliers final: 44 residues processed: 385 average time/residue: 0.5295 time to fit residues: 233.9492 Evaluate side-chains 389 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 326 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 23 GLN Chi-restraints excluded: chain L residue 49 VAL 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 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 12 MET 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 211 MET 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 E residue 109 TYR 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 151 LYS Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 129 MET 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: 0.7980 chunk 69 optimal weight: 8.9990 chunk 199 optimal weight: 0.5980 chunk 19 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 214 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.245283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.220586 restraints weight = 15416.074| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 1.20 r_work: 0.4261 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4151 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19250 Z= 0.106 Angle : 0.479 5.467 25960 Z= 0.245 Chirality : 0.043 0.126 2970 Planarity : 0.003 0.038 3260 Dihedral : 4.560 23.041 2618 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.06 % Allowed : 14.08 % Favored : 82.86 % 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: 0.37 (0.18), residues: 2280 helix: 1.83 (0.18), residues: 890 sheet: 0.31 (0.22), residues: 670 loop : -1.88 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 97 TYR 0.013 0.001 TYR A 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/Z covalent geometry : bond 0.00247 / 0.11 (19220) covalent geometry : angle 0.47865 / 0.24 (25960) hydrogen bonds : bond 0.03934 / 2.57 ( 551) hydrogen bonds : angle 4.08325 / 2.75 ( 1653) metal coordination : bond 0.00300 / 0.17 ( 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 410 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 347 time to evaluate : 0.735 Fit side-chains REVERT: A 211 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6237 (mmm) REVERT: K 29 MET cc_start: 0.7188 (mmp) cc_final: 0.6971 (mmp) REVERT: K 37 ARG cc_start: 0.7301 (ptt180) cc_final: 0.7041 (ttp-170) REVERT: L 3 TYR cc_start: 0.7685 (m-80) cc_final: 0.7453 (m-80) REVERT: L 23 GLN cc_start: 0.7521 (pt0) cc_final: 0.7039 (pm20) REVERT: L 37 ARG cc_start: 0.7657 (ttp-170) cc_final: 0.7434 (ttp-170) REVERT: N 23 GLN cc_start: 0.6987 (mt0) cc_final: 0.6755 (pt0) REVERT: N 37 ARG cc_start: 0.7458 (ttp-170) cc_final: 0.7049 (ttp-170) REVERT: N 54 ARG cc_start: 0.6815 (ttp80) cc_final: 0.6545 (ttp80) REVERT: O 51 ASP cc_start: 0.7322 (m-30) cc_final: 0.7077 (m-30) REVERT: P 29 MET cc_start: 0.7305 (mmp) cc_final: 0.7093 (mmp) REVERT: Q 3 TYR cc_start: 0.7688 (m-80) cc_final: 0.7469 (m-80) REVERT: Q 23 GLN cc_start: 0.7183 (pt0) cc_final: 0.6911 (pm20) REVERT: R 46 GLU cc_start: 0.7678 (pt0) cc_final: 0.7168 (pt0) REVERT: T 51 ASP cc_start: 0.7378 (m-30) cc_final: 0.7151 (m-30) REVERT: C 77 SER cc_start: 0.6726 (OUTLIER) cc_final: 0.6251 (m) REVERT: D 211 MET cc_start: 0.6578 (mtm) cc_final: 0.6111 (mmm) REVERT: D 224 LYS cc_start: 0.8066 (mmmt) cc_final: 0.7856 (mtpt) REVERT: E 178 ARG cc_start: 0.8124 (mtt180) cc_final: 0.7829 (mtt180) REVERT: E 211 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6128 (mmm) REVERT: E 225 THR cc_start: 0.8100 (p) cc_final: 0.7651 (t) REVERT: G 137 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6950 (tmm) REVERT: H 140 MET cc_start: 0.8413 (mmm) cc_final: 0.8088 (tpp) REVERT: H 211 MET cc_start: 0.6942 (mtm) cc_final: 0.6349 (mmm) REVERT: I 140 MET cc_start: 0.8318 (mmm) cc_final: 0.8081 (tpp) REVERT: J 129 MET cc_start: 0.7988 (ttm) cc_final: 0.7737 (mtt) REVERT: J 168 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7610 (mp) REVERT: J 211 MET cc_start: 0.6591 (OUTLIER) cc_final: 0.5938 (mmm) REVERT: F 211 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6037 (mmm) outliers start: 63 outliers final: 30 residues processed: 384 average time/residue: 0.5332 time to fit residues: 235.1341 Evaluate side-chains 365 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 328 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 19 VAL Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 76 THR 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 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 D residue 130 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain B residue 168 LEU 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 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 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: 9.9990 chunk 217 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.237203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.210632 restraints weight = 15716.530| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 1.26 r_work: 0.4188 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4084 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19250 Z= 0.200 Angle : 0.611 6.663 25960 Z= 0.307 Chirality : 0.048 0.141 2970 Planarity : 0.004 0.036 3260 Dihedral : 5.176 26.485 2618 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.83 % Allowed : 14.13 % Favored : 82.04 % 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: -0.01 (0.17), residues: 2280 helix: 1.45 (0.17), residues: 880 sheet: 0.22 (0.21), residues: 670 loop : -2.06 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 235 TYR 0.025 0.002 TYR B 109 PHE 0.028 0.003 PHE G 244 TRP 0.005 0.001 TRP M 79 HIS 0.005 0.001 HIS Q 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (19220) covalent geometry : angle 0.61115 / 0.31 (25960) hydrogen bonds : bond 0.05079 / 3.32 ( 551) hydrogen bonds : angle 4.44399 / 2.99 ( 1653) metal coordination : bond 0.00592 / 0.35 ( 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 424 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 345 time to evaluate : 0.727 Fit side-chains REVERT: A 168 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7705 (mp) REVERT: A 211 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6537 (mmm) REVERT: L 3 TYR cc_start: 0.7796 (m-80) cc_final: 0.7515 (m-80) REVERT: L 23 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7056 (pm20) REVERT: L 65 PHE cc_start: 0.8323 (m-80) cc_final: 0.7876 (m-10) REVERT: N 37 ARG cc_start: 0.7597 (ttp-170) cc_final: 0.7210 (ttp-170) REVERT: Q 3 TYR cc_start: 0.7744 (m-80) cc_final: 0.7456 (m-80) REVERT: R 46 GLU cc_start: 0.7572 (pt0) cc_final: 0.7019 (pt0) REVERT: S 12 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.5691 (pmt) REVERT: S 37 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7318 (ttp-170) REVERT: C 77 SER cc_start: 0.6789 (OUTLIER) cc_final: 0.6289 (m) REVERT: C 154 ILE cc_start: 0.8698 (mt) cc_final: 0.8468 (mm) REVERT: C 183 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6574 (mt-10) REVERT: D 183 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6652 (mt-10) REVERT: D 211 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6607 (mmm) REVERT: E 168 LEU cc_start: 0.7899 (mt) cc_final: 0.7334 (tp) REVERT: E 178 ARG cc_start: 0.8120 (mtt180) cc_final: 0.7907 (mtt180) REVERT: E 211 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6191 (mmm) REVERT: G 211 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.6039 (OUTLIER) REVERT: H 129 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7499 (mmt) REVERT: H 140 MET cc_start: 0.8396 (mmm) cc_final: 0.8047 (tpp) REVERT: H 211 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6499 (mmm) REVERT: J 128 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.6924 (pp20) REVERT: J 129 MET cc_start: 0.8185 (ttm) cc_final: 0.7655 (mtt) REVERT: J 168 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7579 (mp) REVERT: J 211 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6681 (mmm) REVERT: F 211 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6386 (mmm) outliers start: 79 outliers final: 43 residues processed: 387 average time/residue: 0.4994 time to fit residues: 223.1906 Evaluate side-chains 391 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 334 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 149 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain E residue 109 TYR 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 G residue 149 VAL Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 211 MET Chi-restraints excluded: chain H residue 129 MET 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 H residue 228 SER Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 181 VAL 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 137 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: 2.9990 chunk 165 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 195 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 174 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.242616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.216879 restraints weight = 15626.859| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 1.25 r_work: 0.4254 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4153 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19250 Z= 0.104 Angle : 0.478 5.050 25960 Z= 0.244 Chirality : 0.043 0.129 2970 Planarity : 0.003 0.038 3260 Dihedral : 4.566 22.899 2618 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.38 % Allowed : 15.92 % Favored : 81.70 % 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: 0.51 (0.18), residues: 2280 helix: 1.94 (0.17), residues: 890 sheet: 0.34 (0.22), residues: 670 loop : -1.76 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 249 TYR 0.016 0.001 TYR A 109 PHE 0.025 0.002 PHE G 244 TRP 0.006 0.001 TRP K 79 HIS 0.006 0.001 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (19220) covalent geometry : angle 0.47762 / 0.24 (25960) hydrogen bonds : bond 0.03937 / 2.57 ( 551) hydrogen bonds : angle 4.12568 / 2.78 ( 1653) metal coordination : bond 0.00363 / 0.20 ( 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 398 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 349 time to evaluate : 0.751 Fit side-chains REVERT: A 211 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6247 (mmm) REVERT: L 3 TYR cc_start: 0.7763 (m-80) cc_final: 0.7541 (m-80) REVERT: L 37 ARG cc_start: 0.7731 (ttp-170) cc_final: 0.7340 (ttp-170) REVERT: N 37 ARG cc_start: 0.7539 (ttp-170) cc_final: 0.7164 (ttp-170) REVERT: Q 3 TYR cc_start: 0.7739 (m-80) cc_final: 0.7500 (m-80) REVERT: Q 46 GLU cc_start: 0.7406 (pt0) cc_final: 0.7131 (pt0) REVERT: R 46 GLU cc_start: 0.7625 (pt0) cc_final: 0.7127 (pt0) REVERT: S 37 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7193 (ptt180) REVERT: C 77 SER cc_start: 0.6599 (OUTLIER) cc_final: 0.6066 (m) REVERT: C 183 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6550 (mt-10) REVERT: D 183 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6635 (mt-10) REVERT: D 211 MET cc_start: 0.6527 (mtm) cc_final: 0.6282 (mmm) REVERT: E 128 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.6888 (pp20) REVERT: E 178 ARG cc_start: 0.8071 (mtt180) cc_final: 0.7755 (mtt180) REVERT: E 211 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.6022 (mmm) REVERT: E 225 THR cc_start: 0.8047 (p) cc_final: 0.7605 (t) REVERT: H 140 MET cc_start: 0.8298 (mmm) cc_final: 0.7915 (tpp) REVERT: H 211 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6345 (mmm) REVERT: J 168 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7609 (mp) REVERT: J 211 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6231 (mmm) REVERT: F 211 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6185 (mmm) outliers start: 49 outliers final: 30 residues processed: 382 average time/residue: 0.5083 time to fit residues: 223.3747 Evaluate side-chains 369 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 330 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR 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 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 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 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 B residue 109 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 129 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 4 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.240920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.214796 restraints weight = 15535.469| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 1.25 r_work: 0.4229 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4128 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19250 Z= 0.133 Angle : 0.518 7.775 25960 Z= 0.262 Chirality : 0.044 0.137 2970 Planarity : 0.003 0.037 3260 Dihedral : 4.709 23.661 2618 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.86 % Allowed : 15.87 % Favored : 81.26 % 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: 0.49 (0.18), residues: 2280 helix: 1.91 (0.17), residues: 890 sheet: 0.36 (0.22), residues: 670 loop : -1.77 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 178 TYR 0.017 0.001 TYR J 109 PHE 0.025 0.002 PHE C 244 TRP 0.005 0.001 TRP M 79 HIS 0.006 0.001 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (19220) covalent geometry : angle 0.51778 / 0.26 (25960) hydrogen bonds : bond 0.04286 / 2.80 ( 551) hydrogen bonds : angle 4.17909 / 2.81 ( 1653) metal coordination : bond 0.00375 / 0.21 ( 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 397 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 338 time to evaluate : 0.732 Fit side-chains REVERT: A 168 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7716 (mp) REVERT: A 211 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6327 (mmm) REVERT: L 3 TYR cc_start: 0.7703 (m-80) cc_final: 0.7430 (m-80) REVERT: N 37 ARG cc_start: 0.7558 (ttp-170) cc_final: 0.7196 (ttp-170) REVERT: Q 3 TYR cc_start: 0.7741 (m-80) cc_final: 0.7493 (m-80) REVERT: Q 23 GLN cc_start: 0.7634 (pt0) cc_final: 0.7151 (pm20) REVERT: R 46 GLU cc_start: 0.7639 (pt0) cc_final: 0.7136 (pt0) REVERT: S 37 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7201 (ptt180) REVERT: C 77 SER cc_start: 0.6757 (OUTLIER) cc_final: 0.6190 (m) REVERT: C 183 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6713 (mt-10) REVERT: D 128 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7229 (pp20) REVERT: D 183 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6701 (mt-10) REVERT: D 211 MET cc_start: 0.6697 (mtm) cc_final: 0.6451 (mmm) REVERT: E 128 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.6844 (pp20) REVERT: E 178 ARG cc_start: 0.8075 (mtt180) cc_final: 0.7847 (mtt180) REVERT: E 211 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6103 (mmm) REVERT: H 140 MET cc_start: 0.8344 (mmm) cc_final: 0.8010 (tpp) REVERT: H 211 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6312 (mmm) REVERT: J 168 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7617 (mp) REVERT: J 211 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6094 (mmm) REVERT: F 211 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6268 (mmm) outliers start: 59 outliers final: 42 residues processed: 380 average time/residue: 0.5157 time to fit residues: 225.4069 Evaluate side-chains 384 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 331 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 181 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 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 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 5 LEU 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 128 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain B residue 109 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 129 MET 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 181 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: 0.9990 chunk 182 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 145 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.242326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.215960 restraints weight = 15628.447| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 1.28 r_work: 0.4255 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4153 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19250 Z= 0.113 Angle : 0.495 9.250 25960 Z= 0.251 Chirality : 0.043 0.140 2970 Planarity : 0.003 0.038 3260 Dihedral : 4.554 22.768 2618 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.43 % Allowed : 16.50 % Favored : 81.07 % 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: 0.70 (0.18), residues: 2280 helix: 2.11 (0.17), residues: 890 sheet: 0.43 (0.22), residues: 670 loop : -1.65 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 178 TYR 0.015 0.001 TYR J 109 PHE 0.028 0.002 PHE C 244 TRP 0.005 0.001 TRP K 79 HIS 0.005 0.001 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (19220) covalent geometry : angle 0.49517 / 0.25 (25960) hydrogen bonds : bond 0.04041 / 2.65 ( 551) hydrogen bonds : angle 4.11233 / 2.77 ( 1653) metal coordination : bond 0.00374 / 0.21 ( 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 388 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 338 time to evaluate : 0.716 Fit side-chains REVERT: A 168 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7707 (mp) REVERT: A 211 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6251 (mmm) REVERT: L 3 TYR cc_start: 0.7659 (m-80) cc_final: 0.7369 (m-80) REVERT: L 18 MET cc_start: 0.8019 (mmt) cc_final: 0.7618 (mmt) REVERT: N 37 ARG cc_start: 0.7487 (ttp-170) cc_final: 0.7114 (ttp-170) REVERT: Q 3 TYR cc_start: 0.7729 (m-80) cc_final: 0.7476 (m-80) REVERT: R 46 GLU cc_start: 0.7628 (pt0) cc_final: 0.7116 (pt0) REVERT: S 37 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7193 (ptt180) REVERT: T 51 ASP cc_start: 0.7331 (m-30) cc_final: 0.7072 (m-30) REVERT: C 77 SER cc_start: 0.6752 (OUTLIER) cc_final: 0.6217 (m) REVERT: C 183 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6697 (mt-10) REVERT: C 211 MET cc_start: 0.6819 (mtm) cc_final: 0.6231 (mmm) REVERT: D 128 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7161 (pp20) REVERT: D 183 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6682 (mt-10) REVERT: D 211 MET cc_start: 0.6710 (mtm) cc_final: 0.6448 (mmm) REVERT: D 224 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7299 (ttmp) REVERT: B 234 PHE cc_start: 0.8004 (m-80) cc_final: 0.7730 (m-80) REVERT: E 95 PRO cc_start: 0.7503 (Cg_exo) cc_final: 0.7262 (Cg_endo) REVERT: E 128 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.6907 (pp20) REVERT: E 178 ARG cc_start: 0.8050 (mtt180) cc_final: 0.7822 (mtt180) REVERT: E 211 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.5904 (mmm) REVERT: H 140 MET cc_start: 0.8310 (mmm) cc_final: 0.7960 (tpp) REVERT: H 211 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6074 (mmm) REVERT: I 211 MET cc_start: 0.6300 (mtm) cc_final: 0.5859 (mmm) REVERT: J 168 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7623 (mp) REVERT: J 211 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6100 (mmm) REVERT: F 211 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.6212 (mmm) outliers start: 50 outliers final: 37 residues processed: 375 average time/residue: 0.5126 time to fit residues: 220.8887 Evaluate side-chains 376 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 328 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 181 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 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 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 5 LEU 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 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 E residue 128 GLU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 129 MET 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 181 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 41 optimal weight: 8.9990 chunk 133 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 180 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.243706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.217595 restraints weight = 15654.933| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 1.28 r_work: 0.4269 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4170 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19250 Z= 0.102 Angle : 0.475 8.077 25960 Z= 0.242 Chirality : 0.043 0.133 2970 Planarity : 0.003 0.037 3260 Dihedral : 4.417 22.450 2618 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.57 % Allowed : 16.46 % Favored : 80.97 % 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: 0.91 (0.18), residues: 2280 helix: 2.30 (0.17), residues: 890 sheet: 0.49 (0.22), residues: 670 loop : -1.52 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 249 TYR 0.014 0.001 TYR F 109 PHE 0.022 0.002 PHE H 244 TRP 0.006 0.001 TRP S 79 HIS 0.005 0.001 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (19220) covalent geometry : angle 0.47476 / 0.24 (25960) hydrogen bonds : bond 0.03854 / 2.52 ( 551) hydrogen bonds : angle 4.06125 / 2.72 ( 1653) metal coordination : bond 0.00340 / 0.19 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6514.59 seconds wall clock time: 111 minutes 33.20 seconds (6693.20 seconds total)