Starting phenix.real_space_refine on Wed Jul 30 07:41:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7umn_26606/07_2025/7umn_26606_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7umn_26606/07_2025/7umn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7umn_26606/07_2025/7umn_26606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7umn_26606/07_2025/7umn_26606.map" model { file = "/net/cci-nas-00/data/ceres_data/7umn_26606/07_2025/7umn_26606_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7umn_26606/07_2025/7umn_26606_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: "I" 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: "M" 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: C, B, H, J, L, N Time building chain proxies: 6.82, per 1000 atoms: 0.55 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 C 46 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 71 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 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: 3.20 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 2.47 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: 7.03 Time building geometry restraints manager: 3.58 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'I' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'M' selection = chain 'L' 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: 2.100 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: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.360 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.580 ------------------------------------------------------------------------------- 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 : 15.23 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.003 TRP J 99 HIS 0.007 0.003 HIS C 98 PHE 0.055 0.005 PHE B 588 TYR 0.048 0.004 TYR H 107 ARG 0.007 0.001 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.16855 ( 402) hydrogen bonds : angle 8.36885 ( 1053) SS BOND : bond 0.00175 ( 12) SS BOND : angle 3.61656 ( 24) covalent geometry : bond 0.01143 (12705) covalent geometry : angle 0.89305 (17256) *********************** 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 : 1.342 Fit side-chains REVERT: A 56 LEU cc_start: 0.7289 (mt) cc_final: 0.7043 (mt) REVERT: A 158 ASN cc_start: 0.8785 (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: 0.7312 (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: 0.6622 (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: 0.2536 time to fit residues: 75.2422 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 : 1.491 ------------------------------------------------------------------------------- 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 129 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 HIS 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 = 0.160817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136613 restraints weight = 18303.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138847 restraints weight = 13241.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140428 restraints weight = 10606.318| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12717 Z= 0.160 Angle : 0.703 9.194 17280 Z= 0.357 Chirality : 0.046 0.162 1824 Planarity : 0.005 0.065 2217 Dihedral : 6.102 27.383 1720 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.55 % Allowed : 6.93 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.20), residues: 1557 helix: -1.28 (0.39), residues: 156 sheet: -0.15 (0.26), residues: 432 loop : -1.50 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 47 HIS 0.003 0.001 HIS L 34 PHE 0.019 0.002 PHE A 588 TYR 0.022 0.002 TYR I 107 ARG 0.005 0.001 ARG I 98 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 402) hydrogen bonds : angle 6.60335 ( 1053) SS BOND : bond 0.00353 ( 12) SS BOND : angle 1.32212 ( 24) covalent geometry : bond 0.00369 (12705) covalent geometry : angle 0.70176 (17256) *********************** 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 229 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 2.205 Fit side-chains REVERT: B 590 ASP cc_start: 0.5578 (m-30) cc_final: 0.5351 (m-30) REVERT: C 82 TYR cc_start: 0.7504 (p90) cc_final: 0.7216 (p90) REVERT: I 82 GLN cc_start: 0.7191 (tp40) cc_final: 0.6720 (tp40) REVERT: J 51 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.8000 (tp) outliers start: 21 outliers final: 11 residues processed: 219 average time/residue: 0.2607 time to fit residues: 86.8204 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 : 1.451 ------------------------------------------------------------------------------- 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 70 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.158060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135265 restraints weight = 18502.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136946 restraints weight = 14401.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.138063 restraints weight = 12040.003| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12717 Z= 0.169 Angle : 0.656 9.737 17280 Z= 0.336 Chirality : 0.046 0.163 1824 Planarity : 0.005 0.055 2217 Dihedral : 5.637 25.556 1719 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.29 % Allowed : 10.47 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1557 helix: -1.16 (0.39), residues: 159 sheet: -0.09 (0.25), residues: 456 loop : -1.28 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 47 HIS 0.005 0.001 HIS M 34 PHE 0.031 0.002 PHE B 115 TYR 0.018 0.002 TYR I 107 ARG 0.003 0.000 ARG N 24 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 402) hydrogen bonds : angle 6.33941 ( 1053) SS BOND : bond 0.00279 ( 12) SS BOND : angle 0.91013 ( 24) covalent geometry : bond 0.00396 (12705) covalent geometry : angle 0.65560 (17256) *********************** 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 236 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 1.649 Fit side-chains revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7950 (p0) cc_final: 0.7604 (p0) REVERT: B 590 ASP cc_start: 0.5842 (m-30) cc_final: 0.5402 (m-30) REVERT: C 82 TYR cc_start: 0.7544 (p90) cc_final: 0.7258 (p90) REVERT: I 51 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8185 (tp) REVERT: J 98 ARG cc_start: 0.7434 (ttp80) cc_final: 0.6826 (ttp80) outliers start: 31 outliers final: 17 residues processed: 223 average time/residue: 0.3172 time to fit residues: 106.3667 Evaluate side-chains 197 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 2.230 ------------------------------------------------------------------------------- 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 B residue 110 SER Chi-restraints excluded: chain B residue 155 THR 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 581 ASN 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 M residue 58 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 74 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 115 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 108 GLN B 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.156551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133898 restraints weight = 18391.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135466 restraints weight = 14340.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136625 restraints weight = 12133.824| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12717 Z= 0.185 Angle : 0.663 9.727 17280 Z= 0.338 Chirality : 0.046 0.155 1824 Planarity : 0.005 0.051 2217 Dihedral : 5.535 24.665 1719 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.51 % Allowed : 12.61 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.21), residues: 1557 helix: -1.25 (0.38), residues: 156 sheet: 0.08 (0.25), residues: 456 loop : -1.21 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 47 HIS 0.005 0.001 HIS N 34 PHE 0.018 0.002 PHE A 115 TYR 0.017 0.002 TYR H 107 ARG 0.002 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 402) hydrogen bonds : angle 6.29457 ( 1053) SS BOND : bond 0.00352 ( 12) SS BOND : angle 1.50981 ( 24) covalent geometry : bond 0.00438 (12705) covalent geometry : angle 0.66068 (17256) *********************** 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 219 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7884 (p0) cc_final: 0.7676 (p0) REVERT: B 248 ASN cc_start: 0.7804 (t0) cc_final: 0.7545 (t0) REVERT: J 51 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8286 (tp) outliers start: 34 outliers final: 23 residues processed: 203 average time/residue: 0.2096 time to fit residues: 64.2606 Evaluate side-chains 189 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 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 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 114 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 31 optimal weight: 0.0370 chunk 68 optimal weight: 0.9980 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN C 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.157568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.134915 restraints weight = 18517.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135317 restraints weight = 15466.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135908 restraints weight = 13266.958| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12717 Z= 0.163 Angle : 0.644 9.264 17280 Z= 0.326 Chirality : 0.045 0.153 1824 Planarity : 0.004 0.048 2217 Dihedral : 5.443 23.387 1719 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.58 % Allowed : 13.05 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.21), residues: 1557 helix: -1.17 (0.39), residues: 156 sheet: 0.04 (0.25), residues: 462 loop : -1.18 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 47 HIS 0.005 0.001 HIS N 34 PHE 0.018 0.002 PHE C 115 TYR 0.017 0.001 TYR I 107 ARG 0.006 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 402) hydrogen bonds : angle 6.14019 ( 1053) SS BOND : bond 0.00244 ( 12) SS BOND : angle 2.43777 ( 24) covalent geometry : bond 0.00388 (12705) covalent geometry : angle 0.63779 (17256) *********************** 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 227 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7858 (p0) cc_final: 0.7611 (p0) REVERT: A 590 ASP cc_start: 0.5676 (m-30) cc_final: 0.5181 (m-30) REVERT: B 66 LEU cc_start: 0.8080 (mt) cc_final: 0.7691 (mt) REVERT: I 51 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8159 (tp) outliers start: 35 outliers final: 25 residues processed: 210 average time/residue: 0.2178 time to fit residues: 68.5841 Evaluate side-chains 200 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 110 SER Chi-restraints excluded: chain C residue 115 PHE 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 78 THR Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 98 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 11 optimal weight: 0.9990 chunk 149 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 56 optimal weight: 0.2980 chunk 104 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 146 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 117 optimal weight: 0.4980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.159691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136234 restraints weight = 18708.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137932 restraints weight = 14548.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139195 restraints weight = 12092.220| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12717 Z= 0.133 Angle : 0.616 9.682 17280 Z= 0.312 Chirality : 0.044 0.173 1824 Planarity : 0.004 0.046 2217 Dihedral : 5.224 22.325 1719 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.29 % Allowed : 15.19 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.21), residues: 1557 helix: -1.05 (0.40), residues: 156 sheet: 0.29 (0.25), residues: 456 loop : -1.15 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 112 HIS 0.005 0.001 HIS N 34 PHE 0.049 0.002 PHE C 588 TYR 0.017 0.001 TYR I 107 ARG 0.006 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 402) hydrogen bonds : angle 5.91468 ( 1053) SS BOND : bond 0.00234 ( 12) SS BOND : angle 1.82426 ( 24) covalent geometry : bond 0.00310 (12705) covalent geometry : angle 0.61298 (17256) *********************** 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 238 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7818 (p0) cc_final: 0.7528 (p0) REVERT: B 108 GLN cc_start: 0.6923 (pt0) cc_final: 0.6640 (pt0) REVERT: B 187 ASN cc_start: 0.8149 (p0) cc_final: 0.7607 (p0) REVERT: I 51 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8203 (tp) REVERT: I 80 TYR cc_start: 0.7183 (m-80) cc_final: 0.6776 (m-80) outliers start: 31 outliers final: 22 residues processed: 225 average time/residue: 0.2381 time to fit residues: 79.2682 Evaluate side-chains 207 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN 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 C residue 108 GLN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 115 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 51 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 70 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 65 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 108 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** 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 = 0.3977 r_free = 0.3977 target = 0.159021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135591 restraints weight = 18507.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.137315 restraints weight = 14258.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.138486 restraints weight = 11947.508| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12717 Z= 0.147 Angle : 0.631 10.070 17280 Z= 0.321 Chirality : 0.045 0.192 1824 Planarity : 0.004 0.046 2217 Dihedral : 5.189 21.501 1719 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.80 % Allowed : 15.78 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1557 helix: -1.20 (0.39), residues: 156 sheet: 0.39 (0.26), residues: 429 loop : -1.09 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 47 HIS 0.006 0.001 HIS M 34 PHE 0.019 0.002 PHE L 98 TYR 0.026 0.001 TYR A 82 ARG 0.007 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 402) hydrogen bonds : angle 5.96597 ( 1053) SS BOND : bond 0.00181 ( 12) SS BOND : angle 2.20531 ( 24) covalent geometry : bond 0.00342 (12705) covalent geometry : angle 0.62594 (17256) *********************** 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 232 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 187 ASN cc_start: 0.8125 (p0) cc_final: 0.7605 (p0) REVERT: B 248 ASN cc_start: 0.8056 (t0) cc_final: 0.7791 (t0) REVERT: I 51 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8116 (tp) REVERT: I 80 TYR cc_start: 0.7125 (m-80) cc_final: 0.6738 (m-80) REVERT: M 39 LYS cc_start: 0.7211 (mtpt) cc_final: 0.6909 (mmmt) outliers start: 38 outliers final: 29 residues processed: 218 average time/residue: 0.2463 time to fit residues: 80.3098 Evaluate side-chains 212 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 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 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 155 THR 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 51 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 51 ILE 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 17 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 0.0980 chunk 35 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 581 ASN B 581 ASN ** C 108 GLN ** 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 = 0.4007 r_free = 0.4007 target = 0.161644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139843 restraints weight = 18520.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.140554 restraints weight = 15616.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.140770 restraints weight = 12756.605| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12717 Z= 0.121 Angle : 0.614 8.983 17280 Z= 0.315 Chirality : 0.044 0.203 1824 Planarity : 0.004 0.045 2217 Dihedral : 5.064 20.464 1719 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.06 % Allowed : 17.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.21), residues: 1557 helix: -1.32 (0.39), residues: 156 sheet: 0.49 (0.26), residues: 429 loop : -1.03 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 99 HIS 0.005 0.001 HIS L 34 PHE 0.051 0.002 PHE C 588 TYR 0.035 0.001 TYR A 82 ARG 0.008 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 402) hydrogen bonds : angle 5.91591 ( 1053) SS BOND : bond 0.00196 ( 12) SS BOND : angle 2.08722 ( 24) covalent geometry : bond 0.00274 (12705) covalent geometry : angle 0.60909 (17256) *********************** 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 221 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8000 (mt) cc_final: 0.7546 (mt) REVERT: B 248 ASN cc_start: 0.8006 (t0) cc_final: 0.7759 (t0) REVERT: I 51 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8041 (tp) REVERT: I 80 TYR cc_start: 0.7030 (m-80) cc_final: 0.6633 (m-80) REVERT: J 80 TYR cc_start: 0.6844 (m-80) cc_final: 0.6379 (m-80) REVERT: L 89 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7607 (tm-30) outliers start: 28 outliers final: 24 residues processed: 214 average time/residue: 0.2150 time to fit residues: 69.4400 Evaluate side-chains 207 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 213 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 581 ASN Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 92 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 72 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 57 optimal weight: 0.0060 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 108 GLN C 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.162865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140996 restraints weight = 18398.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.141868 restraints weight = 15929.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.142173 restraints weight = 12748.388| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12717 Z= 0.115 Angle : 0.603 7.784 17280 Z= 0.312 Chirality : 0.044 0.199 1824 Planarity : 0.005 0.075 2217 Dihedral : 4.985 20.237 1719 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.06 % Allowed : 17.48 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1557 helix: -1.24 (0.39), residues: 156 sheet: 0.36 (0.25), residues: 468 loop : -0.92 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 99 HIS 0.005 0.001 HIS M 34 PHE 0.047 0.002 PHE B 588 TYR 0.031 0.001 TYR A 82 ARG 0.009 0.000 ARG I 98 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 402) hydrogen bonds : angle 5.81170 ( 1053) SS BOND : bond 0.00184 ( 12) SS BOND : angle 1.95767 ( 24) covalent geometry : bond 0.00259 (12705) covalent geometry : angle 0.59924 (17256) *********************** 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 227 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 1.922 Fit side-chains revert: symmetry clash REVERT: B 248 ASN cc_start: 0.8020 (t0) cc_final: 0.7741 (t0) REVERT: C 66 LEU cc_start: 0.8061 (mt) cc_final: 0.7600 (mt) REVERT: I 51 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8106 (tp) REVERT: I 80 TYR cc_start: 0.6949 (m-80) cc_final: 0.6468 (m-80) REVERT: I 81 MET cc_start: 0.8152 (ttt) cc_final: 0.7885 (ttt) REVERT: J 80 TYR cc_start: 0.6784 (m-80) cc_final: 0.6350 (m-80) REVERT: L 89 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7510 (tm-30) outliers start: 28 outliers final: 24 residues processed: 217 average time/residue: 0.2610 time to fit residues: 86.2657 Evaluate side-chains 211 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 577 MET 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 213 PHE Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 51 ILE 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 48 ILE 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 95 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 581 ASN C 55 GLN C 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.159548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.136274 restraints weight = 18434.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.137934 restraints weight = 14224.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.138867 restraints weight = 11949.111| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12717 Z= 0.164 Angle : 0.649 9.468 17280 Z= 0.333 Chirality : 0.046 0.192 1824 Planarity : 0.005 0.056 2217 Dihedral : 5.108 19.959 1719 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1557 helix: -1.25 (0.40), residues: 156 sheet: 0.31 (0.25), residues: 468 loop : -0.95 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 36 HIS 0.005 0.001 HIS M 34 PHE 0.044 0.002 PHE C 588 TYR 0.026 0.002 TYR A 82 ARG 0.014 0.001 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 402) hydrogen bonds : angle 5.92330 ( 1053) SS BOND : bond 0.00230 ( 12) SS BOND : angle 2.07454 ( 24) covalent geometry : bond 0.00382 (12705) covalent geometry : angle 0.64441 (17256) ********************** 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 214 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: B 248 ASN cc_start: 0.8105 (t0) cc_final: 0.7797 (t0) REVERT: C 66 LEU cc_start: 0.8081 (mt) cc_final: 0.7615 (mt) REVERT: I 51 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8154 (tp) REVERT: I 80 TYR cc_start: 0.6992 (m-80) cc_final: 0.6564 (m-80) REVERT: I 81 MET cc_start: 0.8203 (ttt) cc_final: 0.7796 (ttt) REVERT: J 80 TYR cc_start: 0.6876 (m-80) cc_final: 0.6410 (m-80) REVERT: L 89 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7573 (tm-30) outliers start: 26 outliers final: 23 residues processed: 206 average time/residue: 0.2454 time to fit residues: 78.6742 Evaluate side-chains 207 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 577 MET 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 C residue 580 LEU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain I residue 51 ILE 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 48 ILE 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 101 optimal weight: 0.0070 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 140 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 105 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 68 optimal weight: 0.0570 chunk 143 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN C 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.161965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.140007 restraints weight = 18432.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140226 restraints weight = 15352.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140890 restraints weight = 13416.100| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12717 Z= 0.128 Angle : 0.632 8.979 17280 Z= 0.325 Chirality : 0.045 0.209 1824 Planarity : 0.004 0.047 2217 Dihedral : 5.032 19.814 1719 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.84 % Allowed : 18.58 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1557 helix: -1.25 (0.39), residues: 156 sheet: 0.44 (0.25), residues: 459 loop : -0.91 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 64 HIS 0.005 0.001 HIS M 34 PHE 0.046 0.002 PHE B 588 TYR 0.028 0.001 TYR I 32 ARG 0.012 0.000 ARG J 98 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 402) hydrogen bonds : angle 5.87984 ( 1053) SS BOND : bond 0.00270 ( 12) SS BOND : angle 2.01431 ( 24) covalent geometry : bond 0.00293 (12705) covalent geometry : angle 0.62795 (17256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4414.99 seconds wall clock time: 81 minutes 43.50 seconds (4903.50 seconds total)