Starting phenix.real_space_refine on Thu Sep 26 04:42:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/09_2024/7umn_26606_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/09_2024/7umn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/09_2024/7umn_26606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/09_2024/7umn_26606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/09_2024/7umn_26606_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umn_26606/09_2024/7umn_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-5461/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: 6.16, per 1000 atoms: 0.50 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=4, 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 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: 2.78 Conformation dependent library (CDL) restraints added in 1.5 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: 1.72 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: 4.25 Time building geometry restraints manager: 3.29 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: 6708 14.85 - 29.70: 622 29.70 - 44.55: 124 44.55 - 59.40: 19 59.40 - 74.25: 15 Dihedral angle restraints: 7488 sinusoidal: 2913 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 7485 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: 176 2.60 - 3.18: 11941 3.18 - 3.75: 18628 3.75 - 4.33: 28090 4.33 - 4.90: 46711 Nonbonded interactions: 105546 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 C 282 " pdb=" SG CYS C 306 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 46 " pdb=" SG CYS B 278 " model vdw 2.029 3.760 ... (remaining 105541 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: 0.00 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: 0.830 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 27.870 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.700 ------------------------------------------------------------------------------- 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 12705 Z= 0.754 Angle : 0.893 7.416 17256 Z= 0.499 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 205 time to evaluate : 1.315 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: 0.2319 time to fit residues: 69.2632 Evaluate side-chains 143 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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: 8.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12705 Z= 0.243 Angle : 0.702 9.235 17256 Z= 0.356 Chirality : 0.046 0.161 1824 Planarity : 0.005 0.065 2217 Dihedral : 6.137 27.366 1720 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.84 % Allowed : 6.78 % Favored : 91.37 % 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: -1.63 (0.20), residues: 1557 helix: -1.32 (0.39), residues: 156 sheet: -0.14 (0.26), residues: 432 loop : -1.54 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 47 HIS 0.003 0.001 HIS L 34 PHE 0.020 0.002 PHE A 588 TYR 0.024 0.002 TYR I 107 ARG 0.005 0.001 ARG I 98 *********************** 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 232 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 1.265 Fit side-chains REVERT: B 590 ASP cc_start: 0.5547 (m-30) cc_final: 0.5334 (m-30) REVERT: C 82 TYR cc_start: 0.7572 (p90) cc_final: 0.7297 (p90) REVERT: I 82 GLN cc_start: 0.7195 (tp40) cc_final: 0.6749 (tp40) REVERT: J 51 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.8006 (tp) outliers start: 25 outliers final: 12 residues processed: 221 average time/residue: 0.2117 time to fit residues: 69.8759 Evaluate side-chains 181 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 168 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 L residue 106 LEU 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 77 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 138 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12705 Z= 0.260 Angle : 0.659 9.827 17256 Z= 0.337 Chirality : 0.046 0.164 1824 Planarity : 0.005 0.059 2217 Dihedral : 5.725 25.643 1719 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.36 % Allowed : 10.40 % 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: -1.40 (0.21), residues: 1557 helix: -1.07 (0.39), residues: 159 sheet: -0.09 (0.25), residues: 456 loop : -1.37 (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 N 34 PHE 0.030 0.002 PHE B 115 TYR 0.018 0.002 TYR J 107 ARG 0.003 0.000 ARG N 24 *********************** 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 233 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 1.306 Fit side-chains REVERT: A 187 ASN cc_start: 0.7946 (p0) cc_final: 0.7591 (p0) REVERT: C 82 TYR cc_start: 0.7618 (p90) cc_final: 0.7297 (p90) REVERT: I 51 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8244 (tp) REVERT: I 98 ARG cc_start: 0.7688 (ttp80) cc_final: 0.7056 (ttp80) outliers start: 32 outliers final: 19 residues processed: 221 average time/residue: 0.2101 time to fit residues: 69.9091 Evaluate side-chains 194 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 B residue 278 CYS 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 278 CYS 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 L residue 58 VAL Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 106 LEU 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 137 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 93 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 147 optimal weight: 0.0570 chunk 132 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN C 581 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12705 Z= 0.197 Angle : 0.616 9.407 17256 Z= 0.317 Chirality : 0.045 0.154 1824 Planarity : 0.005 0.054 2217 Dihedral : 5.396 23.819 1719 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.29 % Allowed : 12.54 % Favored : 85.18 % 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: -1.19 (0.21), residues: 1557 helix: -1.07 (0.40), residues: 156 sheet: 0.19 (0.25), residues: 450 loop : -1.27 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 47 HIS 0.005 0.001 HIS N 34 PHE 0.049 0.002 PHE A 588 TYR 0.021 0.001 TYR A 82 ARG 0.006 0.000 ARG J 98 *********************** 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 230 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 1.333 Fit side-chains revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7820 (p0) cc_final: 0.7546 (p0) REVERT: B 248 ASN cc_start: 0.7786 (t0) cc_final: 0.7527 (t0) REVERT: B 590 ASP cc_start: 0.5651 (m-30) cc_final: 0.5268 (m-30) REVERT: H 80 TYR cc_start: 0.7152 (m-80) cc_final: 0.6949 (m-80) REVERT: I 51 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8226 (tp) outliers start: 31 outliers final: 18 residues processed: 219 average time/residue: 0.2158 time to fit residues: 70.9652 Evaluate side-chains 201 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 278 CYS 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 278 CYS 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 L residue 58 VAL Chi-restraints excluded: chain L residue 106 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 0 optimal weight: 0.0370 chunk 75 optimal weight: 0.6980 chunk 132 optimal weight: 40.0000 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 overall best weight: 1.9464 ------------------------------------------------------------------------------- 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 C 55 GLN C 581 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12705 Z= 0.267 Angle : 0.647 10.707 17256 Z= 0.329 Chirality : 0.046 0.154 1824 Planarity : 0.005 0.053 2217 Dihedral : 5.460 22.655 1719 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.51 % Allowed : 14.23 % Favored : 83.26 % 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: -1.21 (0.21), residues: 1557 helix: -1.18 (0.39), residues: 156 sheet: 0.06 (0.25), residues: 462 loop : -1.21 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 47 HIS 0.005 0.001 HIS N 34 PHE 0.025 0.002 PHE A 588 TYR 0.025 0.002 TYR J 60 ARG 0.005 0.000 ARG H 98 *********************** 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 fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 1.373 Fit side-chains revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8123 (mt) cc_final: 0.7737 (mt) outliers start: 34 outliers final: 28 residues processed: 212 average time/residue: 0.2301 time to fit residues: 72.5725 Evaluate side-chains 202 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 278 CYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 278 CYS 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 23 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain J residue 23 LYS 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 L residue 74 THR Chi-restraints excluded: chain L residue 98 PHE 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 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 133 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 142 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** C 581 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12705 Z= 0.200 Angle : 0.611 10.737 17256 Z= 0.310 Chirality : 0.044 0.148 1824 Planarity : 0.004 0.051 2217 Dihedral : 5.273 21.345 1719 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.65 % Allowed : 14.82 % 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: -1.02 (0.21), residues: 1557 helix: -1.00 (0.40), residues: 156 sheet: 0.21 (0.25), residues: 462 loop : -1.10 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 47 HIS 0.006 0.001 HIS N 34 PHE 0.041 0.002 PHE C 588 TYR 0.018 0.001 TYR I 106 ARG 0.005 0.000 ARG J 98 *********************** 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 237 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 187 ASN cc_start: 0.8148 (p0) cc_final: 0.7597 (p0) REVERT: B 590 ASP cc_start: 0.5652 (m-30) cc_final: 0.5249 (m-30) REVERT: I 51 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8238 (tp) REVERT: I 80 TYR cc_start: 0.7134 (m-80) cc_final: 0.6800 (m-80) REVERT: J 51 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8329 (tp) REVERT: M 39 LYS cc_start: 0.7215 (mtpt) cc_final: 0.6913 (mmmt) outliers start: 36 outliers final: 30 residues processed: 222 average time/residue: 0.2214 time to fit residues: 72.8003 Evaluate side-chains 216 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 278 CYS 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 C residue 278 CYS 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 23 LYS 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 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 98 PHE 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 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 16 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 chunk 92 optimal weight: 0.4980 chunk 89 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 GLN C 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12705 Z= 0.172 Angle : 0.593 9.875 17256 Z= 0.304 Chirality : 0.044 0.195 1824 Planarity : 0.004 0.050 2217 Dihedral : 5.096 20.450 1719 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.10 % Allowed : 15.41 % Favored : 81.49 % 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: -1.06 (0.40), residues: 156 sheet: 0.17 (0.24), residues: 498 loop : -0.97 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 47 HIS 0.005 0.001 HIS L 34 PHE 0.017 0.002 PHE C 115 TYR 0.032 0.001 TYR A 82 ARG 0.007 0.000 ARG J 98 *********************** 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 239 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 197 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 ASN cc_start: 0.7625 (t0) cc_final: 0.7419 (t0) REVERT: B 187 ASN cc_start: 0.8105 (p0) cc_final: 0.7547 (p0) REVERT: B 248 ASN cc_start: 0.8081 (t0) cc_final: 0.7812 (t0) REVERT: I 51 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8150 (tp) REVERT: I 74 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7303 (mm-40) REVERT: I 80 TYR cc_start: 0.7040 (m-80) cc_final: 0.6701 (m-80) REVERT: J 51 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8292 (tp) REVERT: J 80 TYR cc_start: 0.6982 (m-80) cc_final: 0.6548 (m-80) outliers start: 42 outliers final: 30 residues processed: 226 average time/residue: 0.2173 time to fit residues: 73.2573 Evaluate side-chains 211 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 278 CYS 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 278 CYS 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 23 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain J residue 23 LYS 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 98 PHE 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 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 58 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 ASN C 108 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12705 Z= 0.254 Angle : 0.634 9.018 17256 Z= 0.326 Chirality : 0.045 0.196 1824 Planarity : 0.004 0.051 2217 Dihedral : 5.206 20.324 1719 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.43 % Allowed : 17.04 % Favored : 80.53 % 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: -0.97 (0.21), residues: 1557 helix: -1.23 (0.40), residues: 156 sheet: 0.27 (0.25), residues: 468 loop : -1.03 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 99 HIS 0.005 0.001 HIS N 34 PHE 0.048 0.002 PHE A 588 TYR 0.027 0.001 TYR A 82 ARG 0.008 0.000 ARG J 98 *********************** 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 fitting. rotamer outliers: 33 poor density : 189 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8052 (mt) cc_final: 0.7599 (mt) REVERT: B 248 ASN cc_start: 0.8086 (t0) cc_final: 0.7806 (t0) REVERT: I 51 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8254 (tp) REVERT: I 74 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7281 (mm-40) REVERT: I 80 TYR cc_start: 0.7052 (m-80) cc_final: 0.6695 (m-80) REVERT: J 51 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8326 (tp) REVERT: J 80 TYR cc_start: 0.6928 (m-80) cc_final: 0.6525 (m-80) REVERT: L 11 MET cc_start: 0.3431 (ttt) cc_final: 0.3107 (ttt) REVERT: L 89 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7554 (tm-30) outliers start: 33 outliers final: 26 residues processed: 213 average time/residue: 0.2275 time to fit residues: 71.8907 Evaluate side-chains 210 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 182 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 213 PHE Chi-restraints excluded: chain B residue 278 CYS 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 213 PHE Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 51 ILE 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 L residue 58 VAL 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 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 128 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 42 optimal weight: 0.0000 chunk 124 optimal weight: 0.0050 chunk 129 optimal weight: 10.0000 chunk 136 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 ASN C 55 GLN C 108 GLN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12705 Z= 0.218 Angle : 0.632 8.898 17256 Z= 0.325 Chirality : 0.045 0.190 1824 Planarity : 0.005 0.075 2217 Dihedral : 5.184 20.279 1719 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.21 % Allowed : 17.11 % 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 (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: -0.97 (0.21), residues: 1557 helix: -1.32 (0.39), residues: 156 sheet: 0.25 (0.25), residues: 468 loop : -1.00 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 47 HIS 0.006 0.001 HIS M 34 PHE 0.046 0.002 PHE A 588 TYR 0.031 0.002 TYR A 82 ARG 0.010 0.001 ARG I 98 *********************** 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 215 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 1.318 Fit side-chains revert: symmetry clash REVERT: B 248 ASN cc_start: 0.8101 (t0) cc_final: 0.7792 (t0) REVERT: I 51 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8282 (tp) REVERT: I 74 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7239 (mm-40) REVERT: I 80 TYR cc_start: 0.7014 (m-80) cc_final: 0.6611 (m-80) REVERT: I 81 MET cc_start: 0.8335 (ttt) cc_final: 0.7934 (ttt) REVERT: J 51 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8295 (tp) REVERT: J 80 TYR cc_start: 0.6911 (m-80) cc_final: 0.6515 (m-80) REVERT: L 89 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7553 (tm-30) outliers start: 30 outliers final: 25 residues processed: 208 average time/residue: 0.2193 time to fit residues: 67.9523 Evaluate side-chains 206 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN 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 213 PHE Chi-restraints excluded: chain B residue 278 CYS 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 213 PHE Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain J residue 23 LYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 152 optimal weight: 0.0000 chunk 140 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 12 optimal weight: 0.0670 chunk 93 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 overall best weight: 0.4922 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN J 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12705 Z= 0.161 Angle : 0.609 8.833 17256 Z= 0.315 Chirality : 0.044 0.211 1824 Planarity : 0.004 0.049 2217 Dihedral : 4.991 20.479 1719 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.84 % Allowed : 17.48 % 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 (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: -0.86 (0.21), residues: 1557 helix: -1.23 (0.39), residues: 156 sheet: 0.20 (0.24), residues: 498 loop : -0.88 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 47 HIS 0.006 0.001 HIS N 34 PHE 0.044 0.002 PHE A 588 TYR 0.028 0.001 TYR A 82 ARG 0.011 0.001 ARG H 98 ********************** 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 219 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 194 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.7956 (mt) cc_final: 0.7504 (mt) REVERT: B 187 ASN cc_start: 0.8067 (p0) cc_final: 0.7626 (p0) REVERT: B 248 ASN cc_start: 0.8079 (t0) cc_final: 0.7765 (t0) REVERT: B 590 ASP cc_start: 0.5239 (m-30) cc_final: 0.4694 (m-30) REVERT: I 51 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8266 (tp) REVERT: I 80 TYR cc_start: 0.6903 (m-80) cc_final: 0.6509 (m-80) REVERT: I 81 MET cc_start: 0.8237 (ttt) cc_final: 0.7970 (ttt) REVERT: J 23 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7969 (tttp) REVERT: J 51 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8253 (tp) REVERT: J 80 TYR cc_start: 0.6763 (m-80) cc_final: 0.6405 (m-80) REVERT: L 89 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7343 (tm-30) REVERT: N 11 MET cc_start: 0.3733 (OUTLIER) cc_final: 0.3222 (ttt) outliers start: 25 outliers final: 17 residues processed: 210 average time/residue: 0.2132 time to fit residues: 67.3146 Evaluate side-chains 202 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 181 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN 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 278 CYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain L residue 58 VAL 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 11 MET 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 129 optimal weight: 0.0050 chunk 37 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 124 optimal weight: 30.0000 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.0030 chunk 106 optimal weight: 2.9990 overall best weight: 1.7608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.158488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135320 restraints weight = 18480.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135807 restraints weight = 15452.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136517 restraints weight = 13900.382| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12705 Z= 0.253 Angle : 0.648 9.128 17256 Z= 0.333 Chirality : 0.046 0.183 1824 Planarity : 0.004 0.050 2217 Dihedral : 5.067 19.779 1719 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.92 % Allowed : 17.85 % 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: -0.88 (0.22), residues: 1557 helix: -1.29 (0.39), residues: 156 sheet: 0.22 (0.24), residues: 498 loop : -0.90 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 47 HIS 0.005 0.001 HIS M 34 PHE 0.042 0.002 PHE C 588 TYR 0.024 0.002 TYR I 106 ARG 0.013 0.001 ARG J 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2424.81 seconds wall clock time: 44 minutes 54.32 seconds (2694.32 seconds total)