Starting phenix.real_space_refine on Sat Jun 28 17:21:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z85_11114/06_2025/6z85_11114.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z85_11114/06_2025/6z85_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_11114/06_2025/6z85_11114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z85_11114/06_2025/6z85_11114.map" model { file = "/net/cci-nas-00/data/ceres_data/6z85_11114/06_2025/6z85_11114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z85_11114/06_2025/6z85_11114.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: M, L, O, N, Q, P, S, R, T, C, B, E, D, G, F, I, H, J Time building chain proxies: 5.11, per 1000 atoms: 0.27 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: 4.02 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.37 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: 3.89 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5043 1.33 - 1.45: 3131 1.45 - 1.57: 10816 1.57 - 1.69: 0 1.69 - 1.81: 230 Bond restraints: 19220 Sorted by residual: bond pdb=" C4A HBI D 302 " pdb=" C8A HBI D 302 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" C4A HBI B 302 " pdb=" C8A HBI B 302 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.46e+00 bond pdb=" C4A HBI J 302 " pdb=" C8A HBI J 302 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C4A HBI F 302 " pdb=" C8A HBI F 302 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C4A HBI I 302 " pdb=" C8A HBI I 302 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.35e+00 ... (remaining 19215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 23761 1.78 - 3.56: 1896 3.56 - 5.34: 273 5.34 - 7.12: 20 7.12 - 8.90: 10 Bond angle restraints: 25960 Sorted by residual: angle pdb=" N GLY I 150 " pdb=" CA GLY I 150 " pdb=" C GLY I 150 " ideal model delta sigma weight residual 111.66 118.57 -6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" N GLY G 150 " pdb=" CA GLY G 150 " pdb=" C GLY G 150 " ideal model delta sigma weight residual 111.66 118.55 -6.89 1.91e+00 2.74e-01 1.30e+01 angle pdb=" N GLY H 150 " pdb=" CA GLY H 150 " pdb=" C GLY H 150 " ideal model delta sigma weight residual 111.66 118.55 -6.89 1.91e+00 2.74e-01 1.30e+01 angle pdb=" N GLY J 150 " pdb=" CA GLY J 150 " pdb=" C GLY J 150 " ideal model delta sigma weight residual 111.66 118.55 -6.89 1.91e+00 2.74e-01 1.30e+01 angle pdb=" N GLY D 150 " pdb=" CA GLY D 150 " pdb=" C GLY D 150 " ideal model delta sigma weight residual 111.66 118.54 -6.88 1.91e+00 2.74e-01 1.30e+01 ... (remaining 25955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 11128 14.52 - 29.03: 482 29.03 - 43.54: 90 43.54 - 58.06: 40 58.06 - 72.57: 10 Dihedral angle restraints: 11750 sinusoidal: 4950 harmonic: 6800 Sorted by residual: dihedral pdb=" CA GLN G 180 " pdb=" C GLN G 180 " pdb=" N VAL G 181 " pdb=" CA VAL G 181 " ideal model delta harmonic sigma weight residual 180.00 148.46 31.54 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA GLN H 180 " pdb=" C GLN H 180 " pdb=" N VAL H 181 " pdb=" CA VAL H 181 " ideal model delta harmonic sigma weight residual 180.00 148.46 31.54 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA GLN B 180 " pdb=" C GLN B 180 " pdb=" N VAL B 181 " pdb=" CA VAL B 181 " ideal model delta harmonic sigma weight residual 180.00 148.47 31.53 0 5.00e+00 4.00e-02 3.98e+01 ... (remaining 11747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1955 0.053 - 0.106: 762 0.106 - 0.159: 203 0.159 - 0.212: 30 0.212 - 0.265: 20 Chirality restraints: 2970 Sorted by residual: chirality pdb=" CB THR L 17 " pdb=" CA THR L 17 " pdb=" OG1 THR L 17 " pdb=" CG2 THR L 17 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB THR N 17 " pdb=" CA THR N 17 " pdb=" OG1 THR N 17 " pdb=" CG2 THR N 17 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB THR O 17 " pdb=" CA THR O 17 " pdb=" OG1 THR O 17 " pdb=" CG2 THR O 17 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2967 not shown) Planarity restraints: 3260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 HBI B 302 " -0.007 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" C4 HBI B 302 " 0.018 2.00e-02 2.50e+03 pdb=" C4A HBI B 302 " 0.006 2.00e-02 2.50e+03 pdb=" C8A HBI B 302 " -0.006 2.00e-02 2.50e+03 pdb=" N1 HBI B 302 " -0.030 2.00e-02 2.50e+03 pdb=" N2 HBI B 302 " -0.006 2.00e-02 2.50e+03 pdb=" N3 HBI B 302 " 0.017 2.00e-02 2.50e+03 pdb=" N5 HBI B 302 " -0.044 2.00e-02 2.50e+03 pdb=" N8 HBI B 302 " 0.044 2.00e-02 2.50e+03 pdb=" O4 HBI B 302 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 HBI I 302 " -0.007 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" C4 HBI I 302 " 0.018 2.00e-02 2.50e+03 pdb=" C4A HBI I 302 " 0.006 2.00e-02 2.50e+03 pdb=" C8A HBI I 302 " -0.006 2.00e-02 2.50e+03 pdb=" N1 HBI I 302 " -0.029 2.00e-02 2.50e+03 pdb=" N2 HBI I 302 " -0.007 2.00e-02 2.50e+03 pdb=" N3 HBI I 302 " 0.017 2.00e-02 2.50e+03 pdb=" N5 HBI I 302 " -0.044 2.00e-02 2.50e+03 pdb=" N8 HBI I 302 " 0.043 2.00e-02 2.50e+03 pdb=" O4 HBI I 302 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 HBI A 302 " 0.007 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" C4 HBI A 302 " -0.018 2.00e-02 2.50e+03 pdb=" C4A HBI A 302 " -0.006 2.00e-02 2.50e+03 pdb=" C8A HBI A 302 " 0.005 2.00e-02 2.50e+03 pdb=" N1 HBI A 302 " 0.030 2.00e-02 2.50e+03 pdb=" N2 HBI A 302 " 0.006 2.00e-02 2.50e+03 pdb=" N3 HBI A 302 " -0.017 2.00e-02 2.50e+03 pdb=" N5 HBI A 302 " 0.044 2.00e-02 2.50e+03 pdb=" N8 HBI A 302 " -0.043 2.00e-02 2.50e+03 pdb=" O4 HBI A 302 " -0.008 2.00e-02 2.50e+03 ... (remaining 3257 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5435 2.82 - 3.34: 15722 3.34 - 3.86: 30516 3.86 - 4.38: 38604 4.38 - 4.90: 66126 Nonbonded interactions: 156403 Sorted by model distance: nonbonded pdb=" OE1 GLN F 182 " pdb=" OG1 THR F 225 " model vdw 2.301 3.040 nonbonded pdb=" OE1 GLN A 182 " pdb=" OG1 THR A 225 " model vdw 2.301 3.040 nonbonded pdb=" OE1 GLN D 182 " pdb=" OG1 THR D 225 " model vdw 2.301 3.040 nonbonded pdb=" OE1 GLN B 182 " pdb=" OG1 THR B 225 " model vdw 2.301 3.040 nonbonded pdb=" OE1 GLN C 182 " pdb=" OG1 THR C 225 " model vdw 2.301 3.040 ... (remaining 156398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.16 Found NCS groups: ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 35.610 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.552 19250 Z= 0.592 Angle : 1.048 8.904 25960 Z= 0.585 Chirality : 0.062 0.265 2970 Planarity : 0.008 0.052 3260 Dihedral : 9.840 72.575 7350 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.49 % Allowed : 1.46 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (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 TRP 0.005 0.002 TRP O 79 HIS 0.008 0.002 HIS D 210 PHE 0.043 0.005 PHE F 234 TYR 0.026 0.004 TYR G 75 ARG 0.010 0.001 ARG C 241 Details of bonding type rmsd hydrogen bonds : bond 0.34261 ( 551) hydrogen bonds : angle 10.28941 ( 1653) metal coordination : bond 0.35286 ( 30) covalent geometry : bond 0.00905 (19220) covalent geometry : angle 1.04802 (25960) *********************** 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 : 2.275 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: 1.2500 time to fit residues: 699.7933 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 : 2.034 ------------------------------------------------------------------------------- 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 194 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN K 42 ASN L 42 ASN M 42 ASN N 42 ASN O 42 ASN P 42 ASN Q 42 ASN R 42 ASN S 42 ASN T 42 ASN C 180 GLN D 180 GLN D 188 GLN B 143 HIS H 143 HIS H 180 GLN I 180 GLN J 143 HIS J 180 GLN F 143 HIS F 180 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.243401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.218302 restraints weight = 15527.311| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 1.21 r_work: 0.4247 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4138 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19250 Z= 0.148 Angle : 0.565 6.432 25960 Z= 0.292 Chirality : 0.045 0.129 2970 Planarity : 0.005 0.044 3260 Dihedral : 7.118 41.340 2720 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.28 % Allowed : 10.19 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.16), residues: 2280 helix: -1.10 (0.16), residues: 880 sheet: -0.21 (0.20), residues: 670 loop : -2.32 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 96 HIS 0.009 0.001 HIS N 31 PHE 0.020 0.002 PHE A 148 TYR 0.012 0.002 TYR J 156 ARG 0.003 0.000 ARG O 63 Details of bonding type rmsd hydrogen bonds : bond 0.05111 ( 551) hydrogen bonds : angle 4.72163 ( 1653) metal coordination : bond 0.00922 ( 30) covalent geometry : bond 0.00349 (19220) covalent geometry : angle 0.56519 (25960) *********************** 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 427 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 380 time to evaluate : 2.054 Fit side-chains REVERT: A 211 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6410 (OUTLIER) REVERT: K 54 ARG cc_start: 0.6610 (ttp-110) cc_final: 0.6248 (ttm110) REVERT: L 37 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7337 (ttp-170) REVERT: L 65 PHE cc_start: 0.7882 (m-10) cc_final: 0.7298 (m-80) REVERT: N 18 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.6822 (mmt) REVERT: N 23 GLN cc_start: 0.7128 (mt0) cc_final: 0.6915 (pt0) REVERT: N 37 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6933 (ptt90) REVERT: O 29 MET cc_start: 0.7125 (mmp) cc_final: 0.6506 (mmp) REVERT: Q 19 VAL cc_start: 0.7953 (m) cc_final: 0.7730 (t) REVERT: C 82 LEU cc_start: 0.6599 (mt) cc_final: 0.6347 (mt) REVERT: C 137 MET cc_start: 0.7017 (tmm) cc_final: 0.6772 (tmm) REVERT: C 143 HIS cc_start: 0.7923 (m170) cc_final: 0.7696 (m170) REVERT: C 173 GLU cc_start: 0.6402 (tt0) cc_final: 0.5646 (tm-30) REVERT: C 211 MET cc_start: 0.6502 (OUTLIER) cc_final: 0.5851 (mmm) REVERT: D 225 THR cc_start: 0.8139 (p) cc_final: 0.7712 (m) REVERT: B 136 ASP cc_start: 0.6603 (m-30) cc_final: 0.6350 (m-30) REVERT: B 177 ARG cc_start: 0.7429 (mmt180) cc_final: 0.6002 (mpt180) REVERT: B 236 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7317 (mt-10) REVERT: E 140 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7851 (mmm) REVERT: E 225 THR cc_start: 0.8232 (p) cc_final: 0.7950 (t) REVERT: G 236 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7281 (mt-10) REVERT: H 225 THR cc_start: 0.8292 (p) cc_final: 0.7962 (m) REVERT: I 225 THR cc_start: 0.8180 (p) cc_final: 0.7794 (m) REVERT: J 143 HIS cc_start: 0.7877 (m-70) cc_final: 0.7664 (m90) REVERT: J 178 ARG cc_start: 0.8162 (mtt180) cc_final: 0.7919 (mtt180) REVERT: J 211 MET cc_start: 0.6250 (OUTLIER) cc_final: 0.5565 (mmm) REVERT: J 242 GLU cc_start: 0.7414 (tt0) cc_final: 0.7108 (mt-10) REVERT: F 140 MET cc_start: 0.8223 (mmm) cc_final: 0.7968 (mmm) REVERT: F 225 THR cc_start: 0.8211 (p) cc_final: 0.7922 (m) outliers start: 47 outliers final: 19 residues processed: 402 average time/residue: 1.0875 time to fit residues: 500.2424 Evaluate side-chains 375 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 350 time to evaluate : 2.022 ------------------------------------------------------------------------------- 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 140 MET 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 216 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 HIS C 180 GLN E 143 HIS H 143 HIS I 180 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.241386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.215473 restraints weight = 15210.088| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 1.24 r_work: 0.4240 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4133 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19250 Z= 0.160 Angle : 0.565 5.480 25960 Z= 0.290 Chirality : 0.046 0.136 2970 Planarity : 0.004 0.040 3260 Dihedral : 6.731 40.513 2718 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.96 % Allowed : 12.18 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2280 helix: 0.50 (0.17), residues: 880 sheet: 0.40 (0.22), residues: 610 loop : -2.39 (0.17), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 79 HIS 0.010 0.001 HIS Q 31 PHE 0.020 0.002 PHE A 148 TYR 0.014 0.002 TYR B 109 ARG 0.003 0.000 ARG I 97 Details of bonding type rmsd hydrogen bonds : bond 0.04952 ( 551) hydrogen bonds : angle 4.37805 ( 1653) metal coordination : bond 0.00644 ( 30) covalent geometry : bond 0.00380 (19220) covalent geometry : angle 0.56538 (25960) *********************** 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 416 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 355 time to evaluate : 1.947 Fit side-chains REVERT: A 211 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6355 (mmm) REVERT: L 37 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7397 (ttp-170) REVERT: N 18 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.6693 (mmt) REVERT: O 29 MET cc_start: 0.6946 (mmp) cc_final: 0.6389 (mmp) REVERT: Q 23 GLN cc_start: 0.7336 (pt0) cc_final: 0.6911 (pm20) REVERT: S 37 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7093 (ptt180) REVERT: T 29 MET cc_start: 0.7023 (mmp) cc_final: 0.6388 (mmp) REVERT: C 77 SER cc_start: 0.6640 (OUTLIER) cc_final: 0.5870 (m) REVERT: C 82 LEU cc_start: 0.6403 (mt) cc_final: 0.6196 (mt) REVERT: C 211 MET cc_start: 0.6721 (OUTLIER) cc_final: 0.6012 (mmm) REVERT: B 136 ASP cc_start: 0.6426 (m-30) cc_final: 0.6181 (m-30) REVERT: B 168 LEU cc_start: 0.7948 (mt) cc_final: 0.7589 (tp) REVERT: E 178 ARG cc_start: 0.8111 (mtt180) cc_final: 0.7792 (mtt180) REVERT: E 211 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.6202 (mmm) REVERT: E 225 THR cc_start: 0.8166 (p) cc_final: 0.7731 (t) REVERT: H 140 MET cc_start: 0.7756 (tpp) cc_final: 0.7537 (tpp) REVERT: H 225 THR cc_start: 0.8332 (p) cc_final: 0.7971 (m) REVERT: I 140 MET cc_start: 0.8184 (mmm) cc_final: 0.7933 (mmm) REVERT: I 211 MET cc_start: 0.5961 (OUTLIER) cc_final: 0.5331 (mmm) REVERT: J 128 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7199 (pp20) REVERT: J 168 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7592 (mp) REVERT: J 211 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.5812 (mmm) REVERT: F 140 MET cc_start: 0.8179 (mmm) cc_final: 0.7899 (tpp) REVERT: F 211 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.5988 (OUTLIER) REVERT: F 225 THR cc_start: 0.8130 (p) cc_final: 0.7804 (m) outliers start: 61 outliers final: 21 residues processed: 383 average time/residue: 1.1181 time to fit residues: 488.8090 Evaluate side-chains 364 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 332 time to evaluate : 1.963 ------------------------------------------------------------------------------- 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 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 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 B residue 82 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 124 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 25 optimal weight: 0.1980 chunk 110 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS C 143 HIS D 180 GLN H 180 GLN J 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.241950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.216183 restraints weight = 15355.340| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 1.24 r_work: 0.4243 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4137 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19250 Z= 0.142 Angle : 0.533 5.015 25960 Z= 0.272 Chirality : 0.045 0.131 2970 Planarity : 0.004 0.039 3260 Dihedral : 6.341 39.644 2718 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.93 % Allowed : 12.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2280 helix: 1.26 (0.18), residues: 880 sheet: 0.21 (0.21), residues: 670 loop : -2.08 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 79 HIS 0.007 0.001 HIS Q 31 PHE 0.021 0.002 PHE E 244 TYR 0.015 0.002 TYR B 109 ARG 0.002 0.000 ARG I 97 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 551) hydrogen bonds : angle 4.25968 ( 1653) metal coordination : bond 0.00454 ( 30) covalent geometry : bond 0.00339 (19220) covalent geometry : angle 0.53317 (25960) *********************** 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 439 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 358 time to evaluate : 2.129 Fit side-chains REVERT: A 211 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6516 (mmm) REVERT: L 23 GLN cc_start: 0.7206 (pt0) cc_final: 0.6809 (pm20) REVERT: L 37 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7350 (ttp-170) REVERT: M 12 MET cc_start: 0.6773 (OUTLIER) cc_final: 0.6041 (pmt) REVERT: N 23 GLN cc_start: 0.7568 (pt0) cc_final: 0.6926 (pm20) REVERT: N 54 ARG cc_start: 0.6800 (ttp80) cc_final: 0.6588 (ttp80) REVERT: O 29 MET cc_start: 0.7127 (mmp) cc_final: 0.6536 (mmp) REVERT: O 37 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7388 (ptt180) REVERT: O 51 ASP cc_start: 0.7393 (m-30) cc_final: 0.7136 (m-30) REVERT: P 12 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6475 (pmt) REVERT: R 46 GLU cc_start: 0.7660 (pt0) cc_final: 0.6910 (pt0) REVERT: S 12 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.5926 (pmt) REVERT: S 37 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7160 (ptt180) REVERT: T 29 MET cc_start: 0.7117 (mmp) cc_final: 0.6466 (mmp) REVERT: T 51 ASP cc_start: 0.7357 (m-30) cc_final: 0.7124 (m-30) REVERT: C 77 SER cc_start: 0.6818 (OUTLIER) cc_final: 0.6026 (m) REVERT: C 211 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6198 (mmm) REVERT: D 128 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7331 (pp20) REVERT: D 211 MET cc_start: 0.6682 (mtm) cc_final: 0.6185 (mmm) REVERT: E 129 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7799 (mmt) REVERT: E 178 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7829 (mtt180) REVERT: E 211 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6171 (mmm) REVERT: E 225 THR cc_start: 0.8214 (p) cc_final: 0.7756 (t) REVERT: G 143 HIS cc_start: 0.7791 (m170) cc_final: 0.7565 (m90) REVERT: H 225 THR cc_start: 0.8339 (p) cc_final: 0.7942 (m) REVERT: I 211 MET cc_start: 0.5843 (OUTLIER) cc_final: 0.5335 (mmm) REVERT: J 128 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7051 (pp20) REVERT: J 129 MET cc_start: 0.8127 (ttm) cc_final: 0.7523 (mtt) REVERT: J 168 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7543 (mp) REVERT: J 211 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.5727 (mmm) REVERT: F 140 MET cc_start: 0.8201 (mmm) cc_final: 0.7998 (tpp) REVERT: F 211 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.5983 (mmm) REVERT: F 225 THR cc_start: 0.8142 (p) cc_final: 0.7775 (m) outliers start: 81 outliers final: 37 residues processed: 397 average time/residue: 1.1010 time to fit residues: 500.4884 Evaluate side-chains 390 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 336 time to evaluate : 2.139 ------------------------------------------------------------------------------- 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 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 12 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 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 73 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 12 MET Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET 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 92 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 199 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 186 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 127 optimal weight: 0.0060 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.243178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.217385 restraints weight = 15464.311| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 1.25 r_work: 0.4253 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4143 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19250 Z= 0.125 Angle : 0.505 5.037 25960 Z= 0.258 Chirality : 0.044 0.128 2970 Planarity : 0.003 0.039 3260 Dihedral : 5.982 36.778 2718 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.74 % Allowed : 13.06 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2280 helix: 1.66 (0.18), residues: 880 sheet: 0.27 (0.21), residues: 670 loop : -1.85 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 79 HIS 0.006 0.001 HIS Q 31 PHE 0.022 0.002 PHE G 244 TYR 0.014 0.001 TYR B 109 ARG 0.002 0.000 ARG I 97 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 551) hydrogen bonds : angle 4.16309 ( 1653) metal coordination : bond 0.00364 ( 30) covalent geometry : bond 0.00295 (19220) covalent geometry : angle 0.50550 (25960) *********************** 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: 77 poor density : 353 time to evaluate : 2.148 Fit side-chains REVERT: A 211 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6429 (mmm) REVERT: L 3 TYR cc_start: 0.7707 (m-80) cc_final: 0.7455 (m-80) REVERT: L 37 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7332 (ttp-170) REVERT: L 46 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7182 (pt0) REVERT: M 12 MET cc_start: 0.6750 (OUTLIER) cc_final: 0.6071 (pmt) REVERT: M 46 GLU cc_start: 0.7612 (pt0) cc_final: 0.7134 (pt0) REVERT: N 12 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.5648 (pmt) REVERT: N 23 GLN cc_start: 0.7469 (pt0) cc_final: 0.6973 (pm20) REVERT: N 37 ARG cc_start: 0.7393 (ttp-170) cc_final: 0.7060 (ttp-170) REVERT: P 29 MET cc_start: 0.7244 (mmp) cc_final: 0.6896 (mmp) REVERT: Q 23 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6888 (pm20) REVERT: R 46 GLU cc_start: 0.7644 (pt0) cc_final: 0.7028 (pt0) REVERT: S 12 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.5991 (pmt) REVERT: T 51 ASP cc_start: 0.7352 (m-30) cc_final: 0.7121 (m-30) REVERT: C 77 SER cc_start: 0.6508 (OUTLIER) cc_final: 0.6047 (m) REVERT: D 211 MET cc_start: 0.6395 (mtm) cc_final: 0.5967 (mmm) REVERT: B 230 MET cc_start: 0.8068 (mmt) cc_final: 0.7773 (mmt) REVERT: E 129 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7808 (mmt) REVERT: E 178 ARG cc_start: 0.8117 (mtt180) cc_final: 0.7771 (mtt180) REVERT: E 211 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6126 (mmm) REVERT: E 225 THR cc_start: 0.8132 (p) cc_final: 0.7677 (t) REVERT: G 137 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6957 (tmm) REVERT: G 143 HIS cc_start: 0.7789 (m170) cc_final: 0.7570 (m90) REVERT: H 129 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7339 (mmt) REVERT: H 211 MET cc_start: 0.6902 (mtm) cc_final: 0.6239 (mmm) REVERT: I 211 MET cc_start: 0.5846 (OUTLIER) cc_final: 0.5330 (mmm) REVERT: J 128 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.6912 (pp20) REVERT: J 129 MET cc_start: 0.8153 (ttm) cc_final: 0.7654 (mtt) REVERT: J 168 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7505 (mp) REVERT: J 211 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.5907 (mmm) REVERT: F 140 MET cc_start: 0.8173 (mmm) cc_final: 0.7946 (tpp) REVERT: F 211 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.5935 (mmm) outliers start: 77 outliers final: 35 residues processed: 391 average time/residue: 1.0785 time to fit residues: 484.3774 Evaluate side-chains 386 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 334 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 23 GLN Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 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 189 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 168 LEU 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 137 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 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 183 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 228 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4587 r_free = 0.4587 target = 0.245178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.220849 restraints weight = 15481.240| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 1.27 r_work: 0.4285 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4181 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19250 Z= 0.102 Angle : 0.472 5.721 25960 Z= 0.241 Chirality : 0.043 0.147 2970 Planarity : 0.003 0.039 3260 Dihedral : 5.505 33.674 2718 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.91 % Allowed : 14.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2280 helix: 1.96 (0.18), residues: 890 sheet: 1.04 (0.24), residues: 560 loop : -1.77 (0.17), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 79 HIS 0.005 0.001 HIS R 31 PHE 0.024 0.002 PHE G 244 TYR 0.011 0.001 TYR B 109 ARG 0.002 0.000 ARG N 54 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 551) hydrogen bonds : angle 4.04113 ( 1653) metal coordination : bond 0.00327 ( 30) covalent geometry : bond 0.00235 (19220) covalent geometry : angle 0.47201 (25960) *********************** 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 409 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 349 time to evaluate : 2.135 Fit side-chains REVERT: A 168 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7696 (mp) REVERT: A 211 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6303 (mmm) REVERT: L 23 GLN cc_start: 0.7499 (pt0) cc_final: 0.6934 (pm20) REVERT: L 37 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7318 (ttp-170) REVERT: L 46 GLU cc_start: 0.7579 (pt0) cc_final: 0.7190 (pt0) REVERT: M 46 GLU cc_start: 0.7544 (pt0) cc_final: 0.7034 (pt0) REVERT: N 23 GLN cc_start: 0.7337 (pt0) cc_final: 0.6838 (pm20) REVERT: N 37 ARG cc_start: 0.7417 (ttp-170) cc_final: 0.6973 (ttp-170) REVERT: O 51 ASP cc_start: 0.7317 (m-30) cc_final: 0.7064 (m-30) REVERT: P 29 MET cc_start: 0.7336 (mmp) cc_final: 0.7097 (mmp) REVERT: Q 23 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.7034 (pm20) REVERT: R 46 GLU cc_start: 0.7686 (pt0) cc_final: 0.7191 (pt0) REVERT: S 37 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6938 (ttp-170) REVERT: T 51 ASP cc_start: 0.7367 (m-30) cc_final: 0.7139 (m-30) REVERT: C 77 SER cc_start: 0.6712 (OUTLIER) cc_final: 0.6244 (m) REVERT: D 224 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7748 (mtpp) REVERT: E 109 TYR cc_start: 0.7665 (OUTLIER) cc_final: 0.7323 (p90) REVERT: E 128 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.6866 (pp20) REVERT: E 129 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7286 (mmt) REVERT: E 178 ARG cc_start: 0.8107 (mtt180) cc_final: 0.7728 (mtt180) REVERT: E 211 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6190 (mmm) REVERT: E 225 THR cc_start: 0.8093 (p) cc_final: 0.7655 (t) REVERT: H 129 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7328 (mmt) REVERT: H 211 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6268 (mmm) REVERT: J 129 MET cc_start: 0.8019 (ttm) cc_final: 0.7796 (mtt) REVERT: J 168 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7686 (mp) REVERT: J 211 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.6080 (mmm) REVERT: F 140 MET cc_start: 0.8101 (mmm) cc_final: 0.7854 (tpp) REVERT: F 211 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.5896 (mmm) outliers start: 60 outliers final: 29 residues processed: 385 average time/residue: 1.1281 time to fit residues: 496.4377 Evaluate side-chains 372 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 328 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain K residue 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 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 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 23 GLN Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain B residue 168 LEU 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 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 211 MET Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 111 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 205 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.239568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.213716 restraints weight = 15694.860| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 1.23 r_work: 0.4221 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.4121 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19250 Z= 0.169 Angle : 0.568 7.257 25960 Z= 0.287 Chirality : 0.046 0.136 2970 Planarity : 0.004 0.040 3260 Dihedral : 6.174 36.840 2718 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.54 % Allowed : 14.17 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2280 helix: 1.69 (0.17), residues: 880 sheet: 0.30 (0.21), residues: 670 loop : -1.93 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 79 HIS 0.004 0.001 HIS O 31 PHE 0.026 0.002 PHE C 244 TYR 0.021 0.002 TYR J 109 ARG 0.003 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04719 ( 551) hydrogen bonds : angle 4.28690 ( 1653) metal coordination : bond 0.00496 ( 30) covalent geometry : bond 0.00408 (19220) covalent geometry : angle 0.56803 (25960) *********************** 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 421 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 348 time to evaluate : 2.020 Fit side-chains REVERT: A 168 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7741 (mp) REVERT: A 211 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6481 (mmm) REVERT: L 23 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.6952 (pm20) REVERT: L 37 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7238 (ttp-170) REVERT: L 65 PHE cc_start: 0.8303 (m-80) cc_final: 0.7984 (m-80) REVERT: L 66 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7214 (mmm-85) REVERT: M 46 GLU cc_start: 0.7578 (pt0) cc_final: 0.7016 (pt0) REVERT: N 23 GLN cc_start: 0.7546 (pt0) cc_final: 0.6996 (pm20) REVERT: N 37 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.7199 (ttp-170) REVERT: N 70 MET cc_start: 0.7521 (tmm) cc_final: 0.7112 (ttp) REVERT: P 12 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6302 (pmt) REVERT: Q 23 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: Q 65 PHE cc_start: 0.7922 (m-80) cc_final: 0.7720 (m-80) REVERT: R 46 GLU cc_start: 0.7562 (pt0) cc_final: 0.7039 (pt0) REVERT: S 37 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7294 (ttp-170) REVERT: C 77 SER cc_start: 0.6724 (OUTLIER) cc_final: 0.6234 (m) REVERT: C 183 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6526 (mt-10) REVERT: D 211 MET cc_start: 0.6726 (mtm) cc_final: 0.6244 (mmm) REVERT: E 128 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.6880 (pp20) REVERT: E 129 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7486 (mmt) REVERT: E 168 LEU cc_start: 0.7954 (mt) cc_final: 0.7401 (tp) REVERT: E 178 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7829 (mtt180) REVERT: E 211 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6193 (mmm) REVERT: E 225 THR cc_start: 0.8136 (p) cc_final: 0.7668 (t) REVERT: G 137 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6986 (tmm) REVERT: H 129 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7653 (mtt) REVERT: H 211 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6519 (mmm) REVERT: I 211 MET cc_start: 0.6434 (mtm) cc_final: 0.5969 (mmm) REVERT: J 128 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.6910 (pp20) REVERT: J 129 MET cc_start: 0.8049 (ttm) cc_final: 0.7718 (mtt) REVERT: J 168 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7612 (mp) REVERT: J 211 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6214 (mmm) REVERT: F 140 MET cc_start: 0.8177 (mmm) cc_final: 0.7934 (tpp) REVERT: F 211 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6349 (mmm) outliers start: 73 outliers final: 40 residues processed: 390 average time/residue: 1.1489 time to fit residues: 514.8563 Evaluate side-chains 392 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 333 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain K residue 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 37 ARG Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 66 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 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 12 MET Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 23 GLN 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 12 MET Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain B residue 168 LEU 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 211 MET Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 149 VAL 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 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 211 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 95 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 25 optimal weight: 0.0980 chunk 167 optimal weight: 0.7980 chunk 229 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.242883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.217179 restraints weight = 15654.091| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 1.25 r_work: 0.4257 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.4156 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19250 Z= 0.111 Angle : 0.485 6.566 25960 Z= 0.248 Chirality : 0.043 0.128 2970 Planarity : 0.003 0.041 3260 Dihedral : 5.652 35.020 2718 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.67 % Allowed : 15.53 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2280 helix: 2.01 (0.18), residues: 890 sheet: 0.39 (0.22), residues: 670 loop : -1.74 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 79 HIS 0.006 0.001 HIS K 31 PHE 0.024 0.002 PHE C 244 TYR 0.015 0.001 TYR J 109 ARG 0.001 0.000 ARG J 178 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 551) hydrogen bonds : angle 4.09344 ( 1653) metal coordination : bond 0.00323 ( 30) covalent geometry : bond 0.00261 (19220) covalent geometry : angle 0.48476 (25960) *********************** 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 407 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 352 time to evaluate : 2.088 Fit side-chains REVERT: A 168 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7694 (mp) REVERT: A 211 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6347 (mmm) REVERT: L 37 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7237 (ttp-170) REVERT: L 65 PHE cc_start: 0.8258 (m-80) cc_final: 0.7925 (m-80) REVERT: M 46 GLU cc_start: 0.7551 (pt0) cc_final: 0.6963 (pt0) REVERT: N 23 GLN cc_start: 0.7437 (pt0) cc_final: 0.6873 (pm20) REVERT: N 37 ARG cc_start: 0.7509 (ttp-170) cc_final: 0.7117 (ttp-170) REVERT: Q 23 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7148 (pm20) REVERT: R 46 GLU cc_start: 0.7600 (pt0) cc_final: 0.7079 (pt0) REVERT: S 37 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7185 (ptt180) REVERT: T 51 ASP cc_start: 0.7342 (m-30) cc_final: 0.7090 (m-30) REVERT: C 77 SER cc_start: 0.6646 (OUTLIER) cc_final: 0.6176 (m) REVERT: C 183 GLU cc_start: 0.6727 (mt-10) cc_final: 0.6436 (mt-10) REVERT: E 109 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.7289 (p90) REVERT: E 128 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.6837 (pp20) REVERT: E 129 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7317 (mmt) REVERT: E 178 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7817 (mtt180) REVERT: E 211 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6118 (mmm) REVERT: E 225 THR cc_start: 0.8054 (p) cc_final: 0.7616 (t) REVERT: G 137 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6870 (tmm) REVERT: H 211 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6542 (mmm) REVERT: I 211 MET cc_start: 0.6305 (mtm) cc_final: 0.5735 (mmm) REVERT: J 168 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7623 (mp) REVERT: J 211 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6239 (mmm) REVERT: F 140 MET cc_start: 0.8146 (mmm) cc_final: 0.7885 (tpp) REVERT: F 211 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6199 (mmm) outliers start: 55 outliers final: 32 residues processed: 386 average time/residue: 1.1108 time to fit residues: 491.2069 Evaluate side-chains 378 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 331 time to evaluate : 2.278 ------------------------------------------------------------------------------- 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 5 LEU 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 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 23 GLN Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain 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 211 MET Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain 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 212 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.242765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.217086 restraints weight = 15645.286| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 1.25 r_work: 0.4256 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4156 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19250 Z= 0.116 Angle : 0.491 6.378 25960 Z= 0.251 Chirality : 0.044 0.137 2970 Planarity : 0.003 0.041 3260 Dihedral : 5.536 34.090 2718 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.91 % Allowed : 15.58 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.18), residues: 2280 helix: 2.10 (0.17), residues: 890 sheet: 0.45 (0.22), residues: 670 loop : -1.67 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 79 HIS 0.006 0.001 HIS K 31 PHE 0.026 0.002 PHE B 244 TYR 0.015 0.001 TYR J 109 ARG 0.002 0.000 ARG J 178 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 551) hydrogen bonds : angle 4.08526 ( 1653) metal coordination : bond 0.00333 ( 30) covalent geometry : bond 0.00273 (19220) covalent geometry : angle 0.49113 (25960) *********************** 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: 60 poor density : 337 time to evaluate : 2.014 Fit side-chains REVERT: A 168 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7693 (mp) REVERT: A 211 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6292 (mmm) REVERT: L 37 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7250 (ttp-170) REVERT: M 46 GLU cc_start: 0.7580 (pt0) cc_final: 0.7119 (pt0) REVERT: N 23 GLN cc_start: 0.7372 (pt0) cc_final: 0.6791 (pm20) REVERT: N 37 ARG cc_start: 0.7515 (ttp-170) cc_final: 0.7138 (ttp-170) REVERT: O 51 ASP cc_start: 0.7289 (m-30) cc_final: 0.7063 (m-30) REVERT: Q 23 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7191 (pm20) REVERT: R 46 GLU cc_start: 0.7643 (pt0) cc_final: 0.7116 (pt0) REVERT: S 37 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7187 (ptt180) REVERT: T 12 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6495 (ptp) REVERT: T 51 ASP cc_start: 0.7332 (m-30) cc_final: 0.7071 (m-30) REVERT: C 77 SER cc_start: 0.6658 (OUTLIER) cc_final: 0.6178 (m) REVERT: D 128 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7085 (pp20) REVERT: D 211 MET cc_start: 0.6352 (mtm) cc_final: 0.5963 (mmm) REVERT: B 234 PHE cc_start: 0.8007 (m-80) cc_final: 0.7718 (m-80) REVERT: E 109 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.7298 (p90) REVERT: E 128 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.6835 (pp20) REVERT: E 129 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7422 (mmt) REVERT: E 178 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7817 (mtt180) REVERT: E 211 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.5976 (mmm) REVERT: E 225 THR cc_start: 0.8062 (p) cc_final: 0.7619 (t) REVERT: G 137 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6912 (tmm) REVERT: H 211 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6488 (mmm) REVERT: I 211 MET cc_start: 0.6184 (mtm) cc_final: 0.5583 (mmm) REVERT: J 168 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7612 (mp) REVERT: J 211 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6277 (mmm) REVERT: F 140 MET cc_start: 0.8102 (mmm) cc_final: 0.7901 (tpp) REVERT: F 211 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6127 (mmm) outliers start: 60 outliers final: 38 residues processed: 375 average time/residue: 1.0971 time to fit residues: 469.0550 Evaluate side-chains 382 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 327 time to evaluate : 1.988 ------------------------------------------------------------------------------- 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 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 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 23 GLN 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 12 MET Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain B residue 168 LEU 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 211 MET Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 149 VAL 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 181 VAL Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 217 optimal weight: 0.7980 chunk 133 optimal weight: 0.0870 chunk 104 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 overall best weight: 0.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4564 r_free = 0.4564 target = 0.243704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.217488 restraints weight = 15803.997| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 1.30 r_work: 0.4272 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4169 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19250 Z= 0.106 Angle : 0.480 7.178 25960 Z= 0.245 Chirality : 0.043 0.140 2970 Planarity : 0.003 0.041 3260 Dihedral : 5.328 32.510 2718 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.67 % Allowed : 16.02 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.18), residues: 2280 helix: 2.24 (0.17), residues: 890 sheet: 0.49 (0.22), residues: 670 loop : -1.60 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 79 HIS 0.006 0.001 HIS K 31 PHE 0.024 0.002 PHE E 244 TYR 0.014 0.001 TYR B 109 ARG 0.002 0.000 ARG J 178 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 551) hydrogen bonds : angle 4.05044 ( 1653) metal coordination : bond 0.00305 ( 30) covalent geometry : bond 0.00249 (19220) covalent geometry : angle 0.47953 (25960) ********************** 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 387 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 332 time to evaluate : 2.027 Fit side-chains REVERT: A 168 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7668 (mp) REVERT: A 211 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6187 (mmm) REVERT: L 18 MET cc_start: 0.8014 (mmt) cc_final: 0.7622 (mmt) REVERT: L 37 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7270 (ttp-170) REVERT: M 46 GLU cc_start: 0.7586 (pt0) cc_final: 0.7161 (pt0) REVERT: N 23 GLN cc_start: 0.7370 (pt0) cc_final: 0.6780 (pm20) REVERT: N 37 ARG cc_start: 0.7483 (ttp-170) cc_final: 0.7109 (ttp-170) REVERT: O 51 ASP cc_start: 0.7268 (m-30) cc_final: 0.7035 (m-30) REVERT: Q 23 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7131 (pm20) REVERT: R 46 GLU cc_start: 0.7620 (pt0) cc_final: 0.7046 (pt0) REVERT: S 37 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7202 (ptt180) REVERT: T 12 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6481 (ptp) REVERT: T 51 ASP cc_start: 0.7303 (m-30) cc_final: 0.7063 (m-30) REVERT: C 77 SER cc_start: 0.6572 (OUTLIER) cc_final: 0.6113 (m) REVERT: C 140 MET cc_start: 0.7733 (mmm) cc_final: 0.7423 (tpp) REVERT: D 128 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.6966 (pp20) REVERT: D 211 MET cc_start: 0.6444 (mtm) cc_final: 0.6005 (mmm) REVERT: E 95 PRO cc_start: 0.7457 (Cg_exo) cc_final: 0.7222 (Cg_endo) REVERT: E 109 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.7198 (p90) REVERT: E 128 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.6830 (pp20) REVERT: E 129 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7473 (mmt) REVERT: E 178 ARG cc_start: 0.8062 (mtt180) cc_final: 0.7771 (mtt180) REVERT: E 211 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.5859 (mmm) REVERT: E 225 THR cc_start: 0.8047 (p) cc_final: 0.7607 (t) REVERT: G 137 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6907 (tmm) REVERT: H 211 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6464 (mmm) REVERT: J 168 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7593 (mp) REVERT: J 211 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6165 (mmm) REVERT: F 211 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6125 (mmm) outliers start: 55 outliers final: 34 residues processed: 368 average time/residue: 1.1019 time to fit residues: 467.6943 Evaluate side-chains 375 residues out of total 2060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 324 time to evaluate : 2.005 ------------------------------------------------------------------------------- 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 19 VAL 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 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 23 GLN 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 12 MET Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain B residue 168 LEU 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 181 VAL 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 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 181 VAL Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 55 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 229 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4539 r_free = 0.4539 target = 0.241057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.214977 restraints weight = 15693.024| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 1.26 r_work: 0.4229 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4127 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19250 Z= 0.142 Angle : 0.531 9.252 25960 Z= 0.269 Chirality : 0.045 0.139 2970 Planarity : 0.003 0.040 3260 Dihedral : 5.708 34.981 2718 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.91 % Allowed : 15.78 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2280 helix: 2.00 (0.17), residues: 890 sheet: 0.42 (0.22), residues: 670 loop : -1.71 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 79 HIS 0.006 0.001 HIS K 31 PHE 0.025 0.002 PHE G 244 TYR 0.018 0.002 TYR J 109 ARG 0.002 0.000 ARG J 178 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 551) hydrogen bonds : angle 4.18427 ( 1653) metal coordination : bond 0.00409 ( 30) covalent geometry : bond 0.00341 (19220) covalent geometry : angle 0.53079 (25960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14235.73 seconds wall clock time: 242 minutes 24.61 seconds (14544.61 seconds total)