Starting phenix.real_space_refine on Wed Mar 4 08:23:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7umn_26606/03_2026/7umn_26606_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7umn_26606/03_2026/7umn_26606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7umn_26606/03_2026/7umn_26606_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7umn_26606/03_2026/7umn_26606_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7umn_26606/03_2026/7umn_26606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7umn_26606/03_2026/7umn_26606.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 7845 2.51 5 N 2073 2.21 5 O 2400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12375 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2392 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 795 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Restraints were copied for chains: B, C, I, J, M, N Time building chain proxies: 2.25, per 1000 atoms: 0.18 Number of scatterers: 12375 At special positions: 0 Unit cell: (110.55, 113.85, 119.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2400 8.00 N 2073 7.00 C 7845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 71 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 562.4 milliseconds 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 36 sheets defined 14.0% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.686A pdb=" N GLU A 78 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 removed outlier: 3.856A pdb=" N GLU A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 574 through 592 Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 74 through 78 removed outlier: 3.686A pdb=" N GLU B 78 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 112 removed outlier: 3.856A pdb=" N GLU B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 574 through 592 Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.686A pdb=" N GLU C 78 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 112 removed outlier: 3.856A pdb=" N GLU C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 112 " --> pdb=" O GLN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 574 through 592 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.613A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.614A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.613A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.755A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE A 83 " --> pdb=" O ILE A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 117 through 118 removed outlier: 7.891A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=AA6, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.906A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.756A pdb=" N LEU B 54 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE B 83 " --> pdb=" O ILE B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 117 through 118 removed outlier: 7.891A pdb=" N LEU B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AB2, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AB3, first strand: chain 'B' and resid 167 through 169 Processing sheet with id=AB4, first strand: chain 'B' and resid 287 through 289 removed outlier: 3.905A pdb=" N CYS B 282 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AB6, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.755A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE C 83 " --> pdb=" O ILE C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 117 through 118 removed outlier: 7.891A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AB9, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC1, first strand: chain 'C' and resid 167 through 169 Processing sheet with id=AC2, first strand: chain 'C' and resid 287 through 289 removed outlier: 3.906A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AC4, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AC5, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.063A pdb=" N ASN H 33 " --> pdb=" O TRP H 99 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN H 52 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE H 57 " --> pdb=" O ASN H 52 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.385A pdb=" N VAL H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.063A pdb=" N ASN I 33 " --> pdb=" O TRP I 99 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET I 34 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN I 52 " --> pdb=" O ILE I 57 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE I 57 " --> pdb=" O ASN I 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.385A pdb=" N VAL I 111 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.063A pdb=" N ASN J 33 " --> pdb=" O TRP J 99 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET J 34 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN J 52 " --> pdb=" O ILE J 57 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE J 57 " --> pdb=" O ASN J 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.385A pdb=" N VAL J 111 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.738A pdb=" N GLU L 17 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR L 77 " --> pdb=" O GLU L 17 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.817A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR L 86 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP L 35 " --> pdb=" O TRP L 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 4 through 7 removed outlier: 5.738A pdb=" N GLU M 17 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR M 77 " --> pdb=" O GLU M 17 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.817A pdb=" N CYS M 88 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY M 101 " --> pdb=" O TYR M 86 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR M 86 " --> pdb=" O GLY M 101 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP M 35 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 4 through 7 removed outlier: 5.737A pdb=" N GLU N 17 " --> pdb=" O THR N 77 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR N 77 " --> pdb=" O GLU N 17 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.817A pdb=" N CYS N 88 " --> pdb=" O GLY N 99 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY N 101 " --> pdb=" O TYR N 86 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR N 86 " --> pdb=" O GLY N 101 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP N 35 " --> pdb=" O TRP N 47 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3948 1.34 - 1.46: 3422 1.46 - 1.59: 5257 1.59 - 1.71: 0 1.71 - 1.83: 78 Bond restraints: 12705 Sorted by residual: bond pdb=" N MET B 577 " pdb=" CA MET B 577 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.23e-02 6.61e+03 1.34e+01 bond pdb=" N MET C 577 " pdb=" CA MET C 577 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.23e-02 6.61e+03 1.34e+01 bond pdb=" N MET A 577 " pdb=" CA MET A 577 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.23e-02 6.61e+03 1.31e+01 bond pdb=" C MET B 577 " pdb=" O MET B 577 " ideal model delta sigma weight residual 1.237 1.279 -0.042 1.19e-02 7.06e+03 1.24e+01 bond pdb=" C MET C 577 " pdb=" O MET C 577 " ideal model delta sigma weight residual 1.237 1.278 -0.042 1.19e-02 7.06e+03 1.22e+01 ... (remaining 12700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 15765 1.48 - 2.97: 1230 2.97 - 4.45: 227 4.45 - 5.93: 22 5.93 - 7.42: 12 Bond angle restraints: 17256 Sorted by residual: angle pdb=" C PHE A 115 " pdb=" CA PHE A 115 " pdb=" CB PHE A 115 " ideal model delta sigma weight residual 112.43 106.10 6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" C PHE B 115 " pdb=" CA PHE B 115 " pdb=" CB PHE B 115 " ideal model delta sigma weight residual 112.43 106.10 6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" C PHE C 115 " pdb=" CA PHE C 115 " pdb=" CB PHE C 115 " ideal model delta sigma weight residual 112.43 106.11 6.32 1.91e+00 2.74e-01 1.09e+01 angle pdb=" CA GLN L 37 " pdb=" CB GLN L 37 " pdb=" CG GLN L 37 " ideal model delta sigma weight residual 114.10 120.56 -6.46 2.00e+00 2.50e-01 1.04e+01 angle pdb=" CA GLN N 37 " pdb=" CB GLN N 37 " pdb=" CG GLN N 37 " ideal model delta sigma weight residual 114.10 120.56 -6.46 2.00e+00 2.50e-01 1.04e+01 ... (remaining 17251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.85: 6718 14.85 - 29.70: 632 29.70 - 44.55: 126 44.55 - 59.40: 21 59.40 - 74.25: 15 Dihedral angle restraints: 7512 sinusoidal: 2937 harmonic: 4575 Sorted by residual: dihedral pdb=" CA PHE B 115 " pdb=" C PHE B 115 " pdb=" N GLU B 116 " pdb=" CA GLU B 116 " ideal model delta harmonic sigma weight residual 180.00 151.38 28.62 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA PHE C 115 " pdb=" C PHE C 115 " pdb=" N GLU C 116 " pdb=" CA GLU C 116 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA PHE A 115 " pdb=" C PHE A 115 " pdb=" N GLU A 116 " pdb=" CA GLU A 116 " ideal model delta harmonic sigma weight residual 180.00 151.41 28.59 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 7509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1630 0.089 - 0.177: 191 0.177 - 0.266: 0 0.266 - 0.354: 0 0.354 - 0.443: 3 Chirality restraints: 1824 Sorted by residual: chirality pdb=" CG LEU A 45 " pdb=" CB LEU A 45 " pdb=" CD1 LEU A 45 " pdb=" CD2 LEU A 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CG LEU C 45 " pdb=" CB LEU C 45 " pdb=" CD1 LEU C 45 " pdb=" CD2 LEU C 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CG LEU B 45 " pdb=" CB LEU B 45 " pdb=" CD1 LEU B 45 " pdb=" CD2 LEU B 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.86e+00 ... (remaining 1821 not shown) Planarity restraints: 2217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 299 " 0.059 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO B 300 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 300 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 300 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 299 " 0.059 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO C 300 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 300 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 300 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 299 " 0.059 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO A 300 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 300 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 300 " 0.049 5.00e-02 4.00e+02 ... (remaining 2214 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 168 2.60 - 3.18: 11925 3.18 - 3.75: 18628 3.75 - 4.33: 28090 4.33 - 4.90: 46711 Nonbonded interactions: 105522 Sorted by model distance: nonbonded pdb=" SG CYS J 22 " pdb=" SG CYS J 96 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS I 22 " pdb=" SG CYS I 96 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " model vdw 2.044 3.760 nonbonded pdb=" SG CYS M 23 " pdb=" SG CYS M 88 " model vdw 2.044 3.760 ... (remaining 105517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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 group one per residue 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.780 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.011 0.074 12717 Z= 0.484 Angle : 0.903 8.057 17280 Z= 0.502 Chirality : 0.056 0.443 1824 Planarity : 0.007 0.089 2217 Dihedral : 12.513 74.250 4572 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.19), residues: 1557 helix: -3.07 (0.34), residues: 132 sheet: -0.46 (0.25), residues: 432 loop : -2.00 (0.17), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 117 TYR 0.048 0.004 TYR H 107 PHE 0.055 0.005 PHE B 588 TRP 0.020 0.003 TRP J 99 HIS 0.007 0.003 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.01143 (12705) covalent geometry : angle 0.89305 (17256) SS BOND : bond 0.00175 ( 12) SS BOND : angle 3.61656 ( 24) hydrogen bonds : bond 0.16855 ( 402) hydrogen bonds : angle 8.36885 ( 1053) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 205 time to evaluate : 0.466 Fit side-chains REVERT: A 56 LEU cc_start: 0.7289 (mt) cc_final: 0.7043 (mt) REVERT: A 158 ASN cc_start: 0.8786 (m-40) cc_final: 0.8570 (m-40) REVERT: B 158 ASN cc_start: 0.8763 (m-40) cc_final: 0.8546 (m-40) REVERT: B 197 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8451 (p) REVERT: B 248 ASN cc_start: 0.7604 (t0) cc_final: 0.7311 (t0) REVERT: H 65 LYS cc_start: 0.7247 (tptt) cc_final: 0.7046 (tptp) REVERT: I 34 MET cc_start: 0.7105 (mmm) cc_final: 0.6621 (mpp) REVERT: I 82 GLN cc_start: 0.7298 (tp40) cc_final: 0.6929 (tp40) REVERT: J 6 GLN cc_start: 0.7531 (mt0) cc_final: 0.6921 (mt0) REVERT: J 82 GLN cc_start: 0.7281 (tp40) cc_final: 0.6962 (tp40) REVERT: L 21 MET cc_start: 0.6347 (ptp) cc_final: 0.6057 (ptt) REVERT: L 89 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7725 (tm-30) REVERT: M 21 MET cc_start: 0.6370 (ptp) cc_final: 0.6133 (ptt) outliers start: 3 outliers final: 0 residues processed: 205 average time/residue: 0.1021 time to fit residues: 30.9883 Evaluate side-chains 143 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 HIS ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.157973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.134535 restraints weight = 18594.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136412 restraints weight = 14043.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137707 restraints weight = 11565.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.138477 restraints weight = 10052.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.139237 restraints weight = 9193.667| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12717 Z= 0.200 Angle : 0.734 9.303 17280 Z= 0.372 Chirality : 0.047 0.163 1824 Planarity : 0.005 0.066 2217 Dihedral : 6.231 27.815 1720 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.62 % Allowed : 7.15 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.20), residues: 1557 helix: -1.52 (0.38), residues: 156 sheet: -0.28 (0.25), residues: 447 loop : -1.61 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 98 TYR 0.025 0.002 TYR I 107 PHE 0.018 0.002 PHE B 588 TRP 0.018 0.002 TRP J 47 HIS 0.003 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00469 (12705) covalent geometry : angle 0.73225 (17256) SS BOND : bond 0.00321 ( 12) SS BOND : angle 1.38977 ( 24) hydrogen bonds : bond 0.04184 ( 402) hydrogen bonds : angle 6.72955 ( 1053) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.453 Fit side-chains REVERT: C 82 TYR cc_start: 0.7628 (p90) cc_final: 0.7357 (p90) REVERT: J 51 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8055 (tp) REVERT: J 81 MET cc_start: 0.8375 (ttt) cc_final: 0.8160 (ttt) outliers start: 22 outliers final: 11 residues processed: 215 average time/residue: 0.0911 time to fit residues: 29.6455 Evaluate side-chains 181 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 100 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN C 581 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.159014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136156 restraints weight = 18676.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137865 restraints weight = 14506.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139025 restraints weight = 12029.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.139475 restraints weight = 10574.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.139475 restraints weight = 9864.227| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12717 Z= 0.148 Angle : 0.648 9.896 17280 Z= 0.331 Chirality : 0.045 0.164 1824 Planarity : 0.005 0.055 2217 Dihedral : 5.667 26.071 1719 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.92 % Allowed : 10.69 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.21), residues: 1557 helix: -1.16 (0.39), residues: 159 sheet: -0.01 (0.26), residues: 447 loop : -1.32 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 106 TYR 0.020 0.001 TYR A 82 PHE 0.030 0.002 PHE A 115 TRP 0.017 0.002 TRP J 47 HIS 0.005 0.001 HIS M 34 Details of bonding type rmsd covalent geometry : bond 0.00346 (12705) covalent geometry : angle 0.64719 (17256) SS BOND : bond 0.00283 ( 12) SS BOND : angle 0.87956 ( 24) hydrogen bonds : bond 0.03693 ( 402) hydrogen bonds : angle 6.36211 ( 1053) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7889 (p0) cc_final: 0.7659 (p0) REVERT: B 590 ASP cc_start: 0.5371 (m-30) cc_final: 0.5148 (m-30) REVERT: C 82 TYR cc_start: 0.7572 (p90) cc_final: 0.7258 (p90) REVERT: I 51 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8115 (tp) REVERT: J 51 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8120 (tp) REVERT: N 73 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8322 (tp) outliers start: 26 outliers final: 13 residues processed: 219 average time/residue: 0.0912 time to fit residues: 30.4840 Evaluate side-chains 186 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 581 ASN C 581 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.154938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.132130 restraints weight = 18551.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.133792 restraints weight = 14503.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.134879 restraints weight = 12207.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135482 restraints weight = 10826.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.135675 restraints weight = 10033.693| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12717 Z= 0.206 Angle : 0.682 9.738 17280 Z= 0.348 Chirality : 0.047 0.157 1824 Planarity : 0.005 0.052 2217 Dihedral : 5.638 23.677 1719 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.80 % Allowed : 12.68 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.21), residues: 1557 helix: -1.45 (0.37), residues: 159 sheet: -0.09 (0.25), residues: 462 loop : -1.22 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 98 TYR 0.019 0.002 TYR J 27 PHE 0.042 0.003 PHE A 588 TRP 0.014 0.002 TRP J 47 HIS 0.005 0.001 HIS N 34 Details of bonding type rmsd covalent geometry : bond 0.00487 (12705) covalent geometry : angle 0.68045 (17256) SS BOND : bond 0.00255 ( 12) SS BOND : angle 1.41206 ( 24) hydrogen bonds : bond 0.03923 ( 402) hydrogen bonds : angle 6.37845 ( 1053) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7923 (p0) cc_final: 0.7722 (p0) REVERT: B 248 ASN cc_start: 0.7787 (t0) cc_final: 0.7524 (t0) REVERT: I 51 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8207 (tp) outliers start: 38 outliers final: 23 residues processed: 201 average time/residue: 0.0952 time to fit residues: 29.2821 Evaluate side-chains 193 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN B 55 GLN C 581 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134539 restraints weight = 18730.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136075 restraints weight = 14550.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.137400 restraints weight = 12290.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137951 restraints weight = 10877.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137951 restraints weight = 10085.672| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12717 Z= 0.149 Angle : 0.631 9.086 17280 Z= 0.321 Chirality : 0.045 0.152 1824 Planarity : 0.004 0.049 2217 Dihedral : 5.419 23.205 1719 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.65 % Allowed : 13.35 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.21), residues: 1557 helix: -1.20 (0.39), residues: 156 sheet: 0.00 (0.25), residues: 462 loop : -1.19 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 98 TYR 0.029 0.001 TYR A 82 PHE 0.048 0.002 PHE C 588 TRP 0.013 0.001 TRP J 47 HIS 0.005 0.001 HIS N 34 Details of bonding type rmsd covalent geometry : bond 0.00353 (12705) covalent geometry : angle 0.62622 (17256) SS BOND : bond 0.00245 ( 12) SS BOND : angle 2.08245 ( 24) hydrogen bonds : bond 0.03560 ( 402) hydrogen bonds : angle 6.13062 ( 1053) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.480 Fit side-chains REVERT: A 187 ASN cc_start: 0.7852 (p0) cc_final: 0.7588 (p0) REVERT: B 108 GLN cc_start: 0.6902 (pt0) cc_final: 0.6592 (pt0) REVERT: B 590 ASP cc_start: 0.5449 (m-30) cc_final: 0.5143 (m-30) REVERT: I 80 TYR cc_start: 0.7210 (m-80) cc_final: 0.6974 (m-80) outliers start: 36 outliers final: 24 residues processed: 212 average time/residue: 0.0923 time to fit residues: 29.8426 Evaluate side-chains 202 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 113 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 GLN C 581 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.159796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137875 restraints weight = 18558.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138657 restraints weight = 14871.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.138619 restraints weight = 12409.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138699 restraints weight = 11791.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.138796 restraints weight = 11482.995| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12717 Z= 0.127 Angle : 0.615 10.754 17280 Z= 0.313 Chirality : 0.045 0.174 1824 Planarity : 0.004 0.046 2217 Dihedral : 5.197 21.387 1719 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.21 % Allowed : 15.41 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.21), residues: 1557 helix: -1.25 (0.39), residues: 156 sheet: 0.15 (0.25), residues: 462 loop : -1.09 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 98 TYR 0.024 0.001 TYR A 82 PHE 0.021 0.002 PHE B 115 TRP 0.012 0.001 TRP I 112 HIS 0.006 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00296 (12705) covalent geometry : angle 0.61219 (17256) SS BOND : bond 0.00228 ( 12) SS BOND : angle 1.76055 ( 24) hydrogen bonds : bond 0.03559 ( 402) hydrogen bonds : angle 5.97415 ( 1053) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.456 Fit side-chains REVERT: B 108 GLN cc_start: 0.6888 (pt0) cc_final: 0.6601 (pt0) REVERT: I 80 TYR cc_start: 0.7196 (m-80) cc_final: 0.6798 (m-80) REVERT: I 98 ARG cc_start: 0.7031 (ttp80) cc_final: 0.6290 (ttp80) REVERT: L 89 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7547 (tm-30) outliers start: 30 outliers final: 20 residues processed: 226 average time/residue: 0.0988 time to fit residues: 33.2518 Evaluate side-chains 205 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 122 optimal weight: 0.3980 chunk 108 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN B 581 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.158926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135618 restraints weight = 18497.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.137310 restraints weight = 14428.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.138338 restraints weight = 12101.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.139254 restraints weight = 10788.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.139579 restraints weight = 9924.529| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12717 Z= 0.141 Angle : 0.619 10.213 17280 Z= 0.316 Chirality : 0.044 0.183 1824 Planarity : 0.004 0.046 2217 Dihedral : 5.153 20.650 1719 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.58 % Allowed : 16.08 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.21), residues: 1557 helix: -1.19 (0.39), residues: 156 sheet: 0.22 (0.25), residues: 459 loop : -1.03 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 98 TYR 0.028 0.001 TYR A 82 PHE 0.052 0.002 PHE B 588 TRP 0.012 0.001 TRP I 36 HIS 0.006 0.001 HIS M 34 Details of bonding type rmsd covalent geometry : bond 0.00328 (12705) covalent geometry : angle 0.61410 (17256) SS BOND : bond 0.00194 ( 12) SS BOND : angle 2.08669 ( 24) hydrogen bonds : bond 0.03614 ( 402) hydrogen bonds : angle 5.91728 ( 1053) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: B 187 ASN cc_start: 0.7879 (p0) cc_final: 0.7642 (p0) REVERT: B 248 ASN cc_start: 0.8009 (t0) cc_final: 0.7782 (t0) REVERT: I 51 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8228 (tp) REVERT: I 74 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7417 (mm-40) REVERT: I 80 TYR cc_start: 0.7137 (m-80) cc_final: 0.6764 (m-80) REVERT: I 98 ARG cc_start: 0.6983 (ttp80) cc_final: 0.6200 (ttp80) REVERT: L 11 MET cc_start: 0.3388 (ttt) cc_final: 0.3100 (ttt) REVERT: M 39 LYS cc_start: 0.7255 (mtpt) cc_final: 0.7011 (mmmt) outliers start: 35 outliers final: 31 residues processed: 211 average time/residue: 0.0938 time to fit residues: 30.1022 Evaluate side-chains 209 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 581 ASN Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN B 55 GLN B 581 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.151648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.129200 restraints weight = 18583.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.129687 restraints weight = 15146.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.130387 restraints weight = 13362.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.130825 restraints weight = 11826.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.131017 restraints weight = 11411.530| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 12717 Z= 0.318 Angle : 0.784 10.786 17280 Z= 0.400 Chirality : 0.049 0.175 1824 Planarity : 0.005 0.049 2217 Dihedral : 5.776 21.133 1719 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.17 % Allowed : 16.15 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.21), residues: 1557 helix: -1.64 (0.38), residues: 156 sheet: -0.07 (0.25), residues: 459 loop : -1.33 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 98 TYR 0.024 0.002 TYR A 82 PHE 0.025 0.003 PHE L 98 TRP 0.023 0.003 TRP C 592 HIS 0.005 0.002 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00748 (12705) covalent geometry : angle 0.77859 (17256) SS BOND : bond 0.00482 ( 12) SS BOND : angle 2.59975 ( 24) hydrogen bonds : bond 0.04267 ( 402) hydrogen bonds : angle 6.48953 ( 1053) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 0.450 Fit side-chains REVERT: B 187 ASN cc_start: 0.8015 (p0) cc_final: 0.7611 (p0) REVERT: B 248 ASN cc_start: 0.8028 (t0) cc_final: 0.7733 (t0) REVERT: I 74 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7347 (mm-40) REVERT: I 98 ARG cc_start: 0.7311 (ttp80) cc_final: 0.6581 (ttp80) REVERT: J 51 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8389 (tp) REVERT: L 11 MET cc_start: 0.3637 (ttt) cc_final: 0.3351 (ttt) REVERT: L 89 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7959 (tm-30) outliers start: 43 outliers final: 29 residues processed: 208 average time/residue: 0.0958 time to fit residues: 30.3343 Evaluate side-chains 197 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 9 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN C 55 GLN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.156848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.133461 restraints weight = 18532.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135150 restraints weight = 14366.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.136091 restraints weight = 12069.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137026 restraints weight = 10778.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.137515 restraints weight = 9913.915| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 12717 Z= 0.157 Angle : 0.659 10.179 17280 Z= 0.334 Chirality : 0.046 0.235 1824 Planarity : 0.004 0.046 2217 Dihedral : 5.419 21.198 1719 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.21 % Allowed : 17.55 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.21), residues: 1557 helix: -1.43 (0.38), residues: 159 sheet: 0.05 (0.25), residues: 459 loop : -1.17 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 98 TYR 0.027 0.001 TYR A 82 PHE 0.035 0.002 PHE C 588 TRP 0.012 0.002 TRP N 47 HIS 0.005 0.001 HIS M 34 Details of bonding type rmsd covalent geometry : bond 0.00369 (12705) covalent geometry : angle 0.65473 (17256) SS BOND : bond 0.00450 ( 12) SS BOND : angle 2.13693 ( 24) hydrogen bonds : bond 0.03623 ( 402) hydrogen bonds : angle 6.18092 ( 1053) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 187 ASN cc_start: 0.8014 (p0) cc_final: 0.7575 (p0) REVERT: B 248 ASN cc_start: 0.7975 (t0) cc_final: 0.7653 (t0) REVERT: B 590 ASP cc_start: 0.5385 (m-30) cc_final: 0.4968 (m-30) REVERT: C 286 GLN cc_start: 0.5446 (OUTLIER) cc_final: 0.4370 (mt0) REVERT: I 80 TYR cc_start: 0.7163 (m-80) cc_final: 0.6828 (m-80) REVERT: I 98 ARG cc_start: 0.7094 (ttp80) cc_final: 0.6342 (ttp80) REVERT: L 89 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7740 (tm-30) outliers start: 30 outliers final: 26 residues processed: 205 average time/residue: 0.0922 time to fit residues: 28.7711 Evaluate side-chains 208 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 142 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 65 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 0.0070 chunk 14 optimal weight: 0.2980 chunk 100 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.160836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139935 restraints weight = 18489.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140311 restraints weight = 13748.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140308 restraints weight = 12180.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140346 restraints weight = 11765.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140512 restraints weight = 11339.119| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12717 Z= 0.120 Angle : 0.619 9.183 17280 Z= 0.318 Chirality : 0.045 0.217 1824 Planarity : 0.004 0.049 2217 Dihedral : 5.106 22.911 1719 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.92 % Allowed : 18.29 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.21), residues: 1557 helix: -1.16 (0.39), residues: 156 sheet: 0.41 (0.25), residues: 447 loop : -1.12 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 98 TYR 0.025 0.001 TYR A 82 PHE 0.045 0.002 PHE C 588 TRP 0.015 0.001 TRP H 112 HIS 0.005 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00268 (12705) covalent geometry : angle 0.61514 (17256) SS BOND : bond 0.00210 ( 12) SS BOND : angle 2.03589 ( 24) hydrogen bonds : bond 0.03523 ( 402) hydrogen bonds : angle 5.89671 ( 1053) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: B 187 ASN cc_start: 0.7998 (p0) cc_final: 0.7533 (p0) REVERT: B 590 ASP cc_start: 0.5469 (m-30) cc_final: 0.4986 (m-30) REVERT: I 80 TYR cc_start: 0.7062 (m-80) cc_final: 0.6576 (m-80) REVERT: I 81 MET cc_start: 0.8372 (ttt) cc_final: 0.8003 (ttt) REVERT: I 98 ARG cc_start: 0.7015 (ttp80) cc_final: 0.6364 (ttp80) REVERT: J 98 ARG cc_start: 0.7288 (ttp80) cc_final: 0.6954 (ttp80) REVERT: L 89 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7440 (tm-30) outliers start: 26 outliers final: 22 residues processed: 214 average time/residue: 0.0855 time to fit residues: 28.3977 Evaluate side-chains 206 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 144 optimal weight: 0.2980 chunk 149 optimal weight: 20.0000 chunk 134 optimal weight: 0.9980 chunk 55 optimal weight: 0.0040 chunk 98 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 147 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 35 ASN ** 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 = 0.4011 r_free = 0.4011 target = 0.161832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140989 restraints weight = 18365.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.141627 restraints weight = 14644.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.141774 restraints weight = 11814.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.141897 restraints weight = 11425.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.141980 restraints weight = 11087.989| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12717 Z= 0.116 Angle : 0.619 8.995 17280 Z= 0.321 Chirality : 0.045 0.216 1824 Planarity : 0.004 0.045 2217 Dihedral : 4.986 25.131 1719 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.40 % Allowed : 19.54 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.21), residues: 1557 helix: -1.25 (0.39), residues: 156 sheet: 0.36 (0.25), residues: 459 loop : -0.97 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 98 TYR 0.022 0.001 TYR A 82 PHE 0.052 0.002 PHE B 588 TRP 0.018 0.001 TRP I 47 HIS 0.006 0.001 HIS N 34 Details of bonding type rmsd covalent geometry : bond 0.00260 (12705) covalent geometry : angle 0.61526 (17256) SS BOND : bond 0.00249 ( 12) SS BOND : angle 1.98884 ( 24) hydrogen bonds : bond 0.03775 ( 402) hydrogen bonds : angle 5.81047 ( 1053) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.59 seconds wall clock time: 32 minutes 34.38 seconds (1954.38 seconds total)