Starting phenix.real_space_refine on Fri Mar 15 19:25:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck1_16689/03_2024/8ck1_16689.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck1_16689/03_2024/8ck1_16689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck1_16689/03_2024/8ck1_16689.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck1_16689/03_2024/8ck1_16689.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck1_16689/03_2024/8ck1_16689.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck1_16689/03_2024/8ck1_16689.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 35 5.16 5 C 7858 2.51 5 N 2132 2.21 5 O 2555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E ASP 207": "OD1" <-> "OD2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12580 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 826, 6419 Classifications: {'peptide': 826} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 794} Chain: "D" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 120} Chain: "B" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 120} Chain: "C" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 120} Chain: "E" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1597 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "F" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1597 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Time building chain proxies: 6.97, per 1000 atoms: 0.55 Number of scatterers: 12580 At special positions: 0 Unit cell: (89.1, 120.15, 207.9, 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 35 16.00 O 2555 8.00 N 2132 7.00 C 7858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 34 " distance=2.03 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 34 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.40 Conformation dependent library (CDL) restraints added in 2.3 seconds 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2966 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 26 sheets defined 22.4% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 23 through 29 removed outlier: 4.257A pdb=" N GLY A 28 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 37 removed outlier: 3.766A pdb=" N ALA A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 310 through 316 removed outlier: 4.079A pdb=" N ARG A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 512 through 516 Processing helix chain 'A' and resid 552 through 555 Processing helix chain 'A' and resid 570 through 574 Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 677 through 681 Processing helix chain 'A' and resid 765 through 769 removed outlier: 3.534A pdb=" N LEU A 769 " --> pdb=" O SER A 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 127 removed outlier: 4.056A pdb=" N VAL D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA D 127 " --> pdb=" O GLN D 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 127 removed outlier: 3.798A pdb=" N VAL B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 102 through 127 removed outlier: 3.511A pdb=" N VAL C 106 " --> pdb=" O TYR C 102 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 127 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 16 removed outlier: 3.693A pdb=" N GLY E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 49 removed outlier: 3.507A pdb=" N ARG E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA E 40 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 53 No H-bonds generated for 'chain 'E' and resid 51 through 53' Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 142 through 163 removed outlier: 4.871A pdb=" N MET E 159 " --> pdb=" O LYS E 155 " (cutoff:3.500A) Proline residue: E 160 - end of helix Processing helix chain 'E' and resid 164 through 189 Processing helix chain 'E' and resid 198 through 203 Processing helix chain 'F' and resid 3 through 16 Processing helix chain 'F' and resid 20 through 24 Processing helix chain 'F' and resid 28 through 49 removed outlier: 4.215A pdb=" N TYR F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 95 through 99 removed outlier: 3.569A pdb=" N GLU F 98 " --> pdb=" O GLY F 95 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE F 99 " --> pdb=" O ALA F 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 95 through 99' Processing helix chain 'F' and resid 142 through 163 removed outlier: 4.628A pdb=" N MET F 159 " --> pdb=" O LYS F 155 " (cutoff:3.500A) Proline residue: F 160 - end of helix Processing helix chain 'F' and resid 164 through 189 Processing helix chain 'F' and resid 198 through 206 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 43 removed outlier: 3.650A pdb=" N SER A 721 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 64 removed outlier: 5.675A pdb=" N PHE A 61 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TYR A 562 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR A 63 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 543 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 536 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 532 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS A 549 " --> pdb=" O PHE A 530 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE A 530 " --> pdb=" O LYS A 549 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 73 through 78 removed outlier: 3.691A pdb=" N GLY A 90 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR A 93 " --> pdb=" O GLY A 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 129 removed outlier: 6.005A pdb=" N HIS A 137 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU A 145 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP A 156 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ARG A 147 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 154 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.784A pdb=" N ILE A 301 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N HIS A 300 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N HIS A 295 " --> pdb=" O HIS A 300 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A 302 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 205 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG A 320 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 235 through 236 Processing sheet with id=AA9, first strand: chain 'A' and resid 335 through 339 Processing sheet with id=AB1, first strand: chain 'A' and resid 390 through 395 removed outlier: 3.642A pdb=" N LEU A 399 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 438 through 440 Processing sheet with id=AB3, first strand: chain 'A' and resid 498 through 500 Processing sheet with id=AB4, first strand: chain 'A' and resid 578 through 582 removed outlier: 4.416A pdb=" N GLY A 580 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 715 " --> pdb=" O GLY A 580 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR A 582 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL A 713 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE A 687 " --> pdb=" O HIS A 694 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 593 through 596 removed outlier: 7.452A pdb=" N ALA A 648 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 666 " --> pdb=" O TYR A 628 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 671 through 674 removed outlier: 6.189A pdb=" N LYS A 672 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 792 through 794 removed outlier: 5.555A pdb=" N ILE A 742 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL A 825 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY A 744 " --> pdb=" O ARG A 823 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.001A pdb=" N GLU A 787 " --> pdb=" O LYS A 751 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 9 through 13 Processing sheet with id=AC1, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AC2, first strand: chain 'B' and resid 9 through 13 Processing sheet with id=AC3, first strand: chain 'B' and resid 20 through 23 Processing sheet with id=AC4, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.929A pdb=" N THR C 82 " --> pdb=" O TYR C 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 55 through 59 removed outlier: 3.649A pdb=" N ASP E 85 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR E 132 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE E 83 " --> pdb=" O THR E 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 61 through 64 removed outlier: 4.615A pdb=" N ALA E 61 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS E 73 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA E 122 " --> pdb=" O HIS E 72 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 55 through 59 removed outlier: 3.766A pdb=" N ASP F 85 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR F 132 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE F 83 " --> pdb=" O THR F 132 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 62 through 64 removed outlier: 7.216A pdb=" N LYS F 73 " --> pdb=" O ILE F 63 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1089 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: 4.70 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4241 1.34 - 1.46: 3037 1.46 - 1.59: 5499 1.59 - 1.72: 0 1.72 - 1.85: 59 Bond restraints: 12836 Sorted by residual: bond pdb=" C VAL A 47 " pdb=" N GLN A 48 " ideal model delta sigma weight residual 1.333 1.403 -0.070 1.39e-02 5.18e+03 2.56e+01 bond pdb=" C GLN A 48 " pdb=" N PRO A 49 " ideal model delta sigma weight residual 1.334 1.425 -0.091 2.34e-02 1.83e+03 1.52e+01 bond pdb=" N ILE D 87 " pdb=" CA ILE D 87 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.22e-02 6.72e+03 8.79e+00 bond pdb=" N VAL A 46 " pdb=" CA VAL A 46 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.17e-02 7.31e+03 8.47e+00 bond pdb=" N ILE A 410 " pdb=" CA ILE A 410 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.21e-02 6.83e+03 7.96e+00 ... (remaining 12831 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.24: 298 106.24 - 113.23: 6792 113.23 - 120.21: 4638 120.21 - 127.19: 5612 127.19 - 134.17: 131 Bond angle restraints: 17471 Sorted by residual: angle pdb=" O VAL A 47 " pdb=" C VAL A 47 " pdb=" N GLN A 48 " ideal model delta sigma weight residual 122.57 127.86 -5.29 1.25e+00 6.40e-01 1.79e+01 angle pdb=" C TYR E 38 " pdb=" N ASP E 39 " pdb=" CA ASP E 39 " ideal model delta sigma weight residual 120.44 115.56 4.88 1.30e+00 5.92e-01 1.41e+01 angle pdb=" C GLY C 59 " pdb=" N ASP C 60 " pdb=" CA ASP C 60 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 angle pdb=" N THR D 51 " pdb=" CA THR D 51 " pdb=" C THR D 51 " ideal model delta sigma weight residual 113.43 108.91 4.52 1.26e+00 6.30e-01 1.29e+01 angle pdb=" N LEU B 95 " pdb=" CA LEU B 95 " pdb=" C LEU B 95 " ideal model delta sigma weight residual 114.56 110.02 4.54 1.27e+00 6.20e-01 1.28e+01 ... (remaining 17466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 6579 17.85 - 35.71: 784 35.71 - 53.56: 200 53.56 - 71.41: 37 71.41 - 89.26: 19 Dihedral angle restraints: 7619 sinusoidal: 2974 harmonic: 4645 Sorted by residual: dihedral pdb=" CA ALA A 777 " pdb=" C ALA A 777 " pdb=" N GLU A 778 " pdb=" CA GLU A 778 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA TRP A 408 " pdb=" C TRP A 408 " pdb=" N MET A 409 " pdb=" CA MET A 409 " ideal model delta harmonic sigma weight residual 180.00 160.40 19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP C 73 " pdb=" C ASP C 73 " pdb=" N PRO C 74 " pdb=" CA PRO C 74 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 7616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1389 0.044 - 0.087: 367 0.087 - 0.131: 160 0.131 - 0.174: 18 0.174 - 0.218: 6 Chirality restraints: 1940 Sorted by residual: chirality pdb=" CA LEU A 659 " pdb=" N LEU A 659 " pdb=" C LEU A 659 " pdb=" CB LEU A 659 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE E 107 " pdb=" N ILE E 107 " pdb=" C ILE E 107 " pdb=" CB ILE E 107 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE E 205 " pdb=" N ILE E 205 " pdb=" C ILE E 205 " pdb=" CB ILE E 205 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.51e-01 ... (remaining 1937 not shown) Planarity restraints: 2322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 203 " 0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C ALA F 203 " -0.057 2.00e-02 2.50e+03 pdb=" O ALA F 203 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN F 204 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR D 102 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO D 103 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 104 " 0.016 2.00e-02 2.50e+03 1.50e-02 4.53e+00 pdb=" CG TYR F 104 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR F 104 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR F 104 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR F 104 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 104 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 104 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 104 " 0.001 2.00e-02 2.50e+03 ... (remaining 2319 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2536 2.77 - 3.30: 12767 3.30 - 3.83: 21314 3.83 - 4.37: 24700 4.37 - 4.90: 41815 Nonbonded interactions: 103132 Sorted by model distance: nonbonded pdb=" O ASP F 207 " pdb=" OD1 ASP F 207 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR B 12 " pdb=" O PRO B 22 " model vdw 2.246 2.440 nonbonded pdb=" OG SER A 384 " pdb=" N ARG A 385 " model vdw 2.257 2.520 nonbonded pdb=" O GLU E 98 " pdb=" ND2 ASN E 193 " model vdw 2.260 2.520 nonbonded pdb=" O GLY A 590 " pdb=" OG SER A 612 " model vdw 2.267 2.440 ... (remaining 103127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 6.220 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 35.250 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.090 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.004 0.091 12836 Z= 0.282 Angle : 0.749 9.938 17471 Z= 0.444 Chirality : 0.047 0.218 1940 Planarity : 0.004 0.062 2322 Dihedral : 16.949 89.264 4647 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.59 % Allowed : 26.21 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.07 (0.21), residues: 1604 helix: 0.51 (0.32), residues: 278 sheet: -1.80 (0.25), residues: 419 loop : -1.78 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 37 HIS 0.005 0.001 HIS F 84 PHE 0.015 0.002 PHE F 53 TYR 0.037 0.002 TYR F 104 ARG 0.004 0.000 ARG F 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 326 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8105 (m-80) REVERT: A 492 GLU cc_start: 0.7998 (tp30) cc_final: 0.6683 (mt-10) REVERT: A 631 ASP cc_start: 0.7167 (m-30) cc_final: 0.6700 (t0) REVERT: D 62 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7338 (tm-30) REVERT: D 68 PHE cc_start: 0.5675 (t80) cc_final: 0.5286 (t80) REVERT: B 67 THR cc_start: 0.8754 (m) cc_final: 0.8500 (t) REVERT: C 92 GLU cc_start: 0.7751 (mp0) cc_final: 0.7535 (mp0) REVERT: C 112 ARG cc_start: 0.8921 (mmt180) cc_final: 0.8533 (mmt180) REVERT: E 27 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7258 (mtpt) REVERT: E 79 ASP cc_start: 0.7581 (p0) cc_final: 0.7338 (p0) REVERT: E 94 ASP cc_start: 0.7228 (t70) cc_final: 0.6789 (t70) REVERT: E 144 ASP cc_start: 0.8980 (p0) cc_final: 0.8724 (p0) REVERT: E 204 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.7233 (t0) REVERT: F 18 ASP cc_start: 0.8619 (t0) cc_final: 0.8272 (p0) outliers start: 8 outliers final: 2 residues processed: 328 average time/residue: 0.2505 time to fit residues: 116.7471 Evaluate side-chains 274 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 270 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 204 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 66 optimal weight: 0.0040 chunk 40 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 overall best weight: 5.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN F 14 ASN F 84 HIS F 188 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12836 Z= 0.306 Angle : 0.617 8.545 17471 Z= 0.325 Chirality : 0.045 0.201 1940 Planarity : 0.004 0.052 2322 Dihedral : 5.059 50.785 1787 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 5.42 % Allowed : 24.94 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.96 (0.20), residues: 1604 helix: 0.82 (0.30), residues: 291 sheet: -1.66 (0.25), residues: 423 loop : -1.88 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 37 HIS 0.005 0.001 HIS F 84 PHE 0.015 0.002 PHE D 21 TYR 0.026 0.002 TYR A 482 ARG 0.004 0.000 ARG D 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 273 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8416 (p) REVERT: A 487 TRP cc_start: 0.8726 (OUTLIER) cc_final: 0.7466 (m-10) REVERT: A 492 GLU cc_start: 0.8176 (tp30) cc_final: 0.7033 (mt-10) REVERT: D 62 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7453 (tm-30) REVERT: B 67 THR cc_start: 0.8648 (m) cc_final: 0.8222 (t) REVERT: B 98 GLN cc_start: 0.7745 (mm110) cc_final: 0.7495 (mm-40) REVERT: B 110 PHE cc_start: 0.8166 (t80) cc_final: 0.7936 (t80) REVERT: B 120 GLN cc_start: 0.8297 (mt0) cc_final: 0.7625 (mt0) REVERT: C 98 GLN cc_start: 0.8531 (mp10) cc_final: 0.8209 (mp10) REVERT: C 101 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: E 27 LYS cc_start: 0.8425 (mtmm) cc_final: 0.7593 (mtpt) REVERT: E 79 ASP cc_start: 0.7904 (p0) cc_final: 0.7534 (p0) REVERT: E 94 ASP cc_start: 0.7152 (t0) cc_final: 0.6880 (t70) REVERT: E 144 ASP cc_start: 0.8965 (p0) cc_final: 0.8685 (p0) REVERT: F 18 ASP cc_start: 0.8718 (t0) cc_final: 0.8397 (p0) REVERT: F 131 TYR cc_start: 0.7621 (p90) cc_final: 0.7100 (p90) REVERT: F 141 MET cc_start: 0.8785 (pmm) cc_final: 0.8439 (pmm) outliers start: 73 outliers final: 45 residues processed: 316 average time/residue: 0.2187 time to fit residues: 101.9990 Evaluate side-chains 303 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 255 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN F 14 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12836 Z= 0.338 Angle : 0.622 9.232 17471 Z= 0.328 Chirality : 0.045 0.204 1940 Planarity : 0.004 0.046 2322 Dihedral : 4.804 20.555 1777 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 6.98 % Allowed : 25.32 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.90 (0.20), residues: 1604 helix: 0.90 (0.30), residues: 294 sheet: -1.57 (0.26), residues: 400 loop : -1.90 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 37 HIS 0.003 0.001 HIS A 523 PHE 0.014 0.002 PHE F 53 TYR 0.022 0.002 TYR C 101 ARG 0.004 0.000 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 264 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8472 (p) REVERT: A 212 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8003 (tp30) REVERT: A 487 TRP cc_start: 0.8700 (OUTLIER) cc_final: 0.7540 (m-10) REVERT: A 492 GLU cc_start: 0.7892 (tp30) cc_final: 0.6736 (mt-10) REVERT: A 670 MET cc_start: 0.7600 (mtm) cc_final: 0.7255 (mtm) REVERT: D 62 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7489 (tm-30) REVERT: B 9 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.7966 (ttm-80) REVERT: B 67 THR cc_start: 0.8725 (m) cc_final: 0.8338 (t) REVERT: B 98 GLN cc_start: 0.8016 (mm110) cc_final: 0.7784 (mm-40) REVERT: B 104 GLU cc_start: 0.8150 (mp0) cc_final: 0.7922 (mp0) REVERT: B 120 GLN cc_start: 0.8091 (mt0) cc_final: 0.7328 (mt0) REVERT: C 6 ASN cc_start: 0.8075 (OUTLIER) cc_final: 0.7861 (t0) REVERT: C 98 GLN cc_start: 0.8600 (mp10) cc_final: 0.8223 (pm20) REVERT: C 101 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: C 112 ARG cc_start: 0.8962 (mmt180) cc_final: 0.8379 (mmt180) REVERT: E 27 LYS cc_start: 0.8638 (mtmm) cc_final: 0.7884 (mtpt) REVERT: E 79 ASP cc_start: 0.7939 (p0) cc_final: 0.7627 (p0) REVERT: E 144 ASP cc_start: 0.8962 (p0) cc_final: 0.8661 (p0) REVERT: F 18 ASP cc_start: 0.8776 (t0) cc_final: 0.8418 (p0) REVERT: F 32 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7382 (mtt-85) REVERT: F 106 GLN cc_start: 0.8867 (mm110) cc_final: 0.8522 (mm110) REVERT: F 131 TYR cc_start: 0.7866 (p90) cc_final: 0.7278 (p90) REVERT: F 159 MET cc_start: 0.8154 (tpp) cc_final: 0.7950 (mmt) outliers start: 94 outliers final: 67 residues processed: 329 average time/residue: 0.2248 time to fit residues: 108.7905 Evaluate side-chains 323 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 249 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 199 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 41 optimal weight: 0.0770 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN F 14 ASN F 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12836 Z= 0.166 Angle : 0.549 10.189 17471 Z= 0.287 Chirality : 0.043 0.211 1940 Planarity : 0.004 0.037 2322 Dihedral : 4.368 20.080 1777 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.31 % Allowed : 28.36 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.55 (0.21), residues: 1604 helix: 1.44 (0.30), residues: 289 sheet: -1.33 (0.26), residues: 397 loop : -1.76 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 520 HIS 0.003 0.001 HIS F 84 PHE 0.019 0.001 PHE B 21 TYR 0.023 0.001 TYR C 53 ARG 0.003 0.000 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 281 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8439 (m-80) REVERT: A 487 TRP cc_start: 0.8362 (OUTLIER) cc_final: 0.7310 (m-10) REVERT: A 670 MET cc_start: 0.7565 (mtm) cc_final: 0.7197 (mtm) REVERT: B 9 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7989 (ttm-80) REVERT: B 21 PHE cc_start: 0.9133 (m-80) cc_final: 0.8863 (m-80) REVERT: B 67 THR cc_start: 0.8567 (m) cc_final: 0.8181 (t) REVERT: B 92 GLU cc_start: 0.7574 (tp30) cc_final: 0.7359 (tp30) REVERT: B 104 GLU cc_start: 0.8128 (mp0) cc_final: 0.7857 (mp0) REVERT: B 120 GLN cc_start: 0.8167 (mt0) cc_final: 0.7658 (mt0) REVERT: C 48 ILE cc_start: 0.9054 (mm) cc_final: 0.8820 (mt) REVERT: C 101 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: E 27 LYS cc_start: 0.8375 (mtmm) cc_final: 0.7580 (mtpt) REVERT: E 79 ASP cc_start: 0.7815 (p0) cc_final: 0.7415 (p0) REVERT: E 144 ASP cc_start: 0.8970 (p0) cc_final: 0.8589 (p0) REVERT: E 159 MET cc_start: 0.8600 (tpt) cc_final: 0.7038 (ttp) REVERT: F 18 ASP cc_start: 0.8688 (t0) cc_final: 0.8383 (p0) REVERT: F 131 TYR cc_start: 0.7780 (p90) cc_final: 0.6924 (p90) REVERT: F 156 ASN cc_start: 0.8776 (t0) cc_final: 0.8525 (t0) REVERT: F 161 MET cc_start: 0.8837 (tpp) cc_final: 0.8537 (tpp) outliers start: 58 outliers final: 33 residues processed: 321 average time/residue: 0.2306 time to fit residues: 107.8505 Evaluate side-chains 293 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 256 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 207 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 2 optimal weight: 0.0060 chunk 113 optimal weight: 30.0000 chunk 63 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 137 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 overall best weight: 6.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12836 Z= 0.350 Angle : 0.636 10.571 17471 Z= 0.333 Chirality : 0.045 0.216 1940 Planarity : 0.004 0.042 2322 Dihedral : 4.742 20.075 1777 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 6.31 % Allowed : 27.17 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.71 (0.20), residues: 1604 helix: 1.32 (0.30), residues: 284 sheet: -1.47 (0.25), residues: 402 loop : -1.83 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 216 HIS 0.005 0.001 HIS F 84 PHE 0.014 0.002 PHE F 53 TYR 0.022 0.002 TYR C 101 ARG 0.005 0.001 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 266 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8743 (m-80) REVERT: A 54 SER cc_start: 0.9072 (OUTLIER) cc_final: 0.8520 (p) REVERT: A 199 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8780 (t) REVERT: A 487 TRP cc_start: 0.8779 (OUTLIER) cc_final: 0.7624 (m-10) REVERT: A 759 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8449 (tpt-90) REVERT: A 776 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7174 (m-30) REVERT: A 809 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: D 82 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7822 (p) REVERT: D 119 GLN cc_start: 0.8967 (pp30) cc_final: 0.8733 (pp30) REVERT: B 9 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8020 (ttm-80) REVERT: B 67 THR cc_start: 0.8650 (m) cc_final: 0.8237 (t) REVERT: B 92 GLU cc_start: 0.7679 (tp30) cc_final: 0.7352 (tp30) REVERT: B 104 GLU cc_start: 0.8115 (mp0) cc_final: 0.7852 (mp0) REVERT: B 120 GLN cc_start: 0.8179 (mt0) cc_final: 0.7373 (mt0) REVERT: C 48 ILE cc_start: 0.9126 (mm) cc_final: 0.8858 (mt) REVERT: C 91 GLN cc_start: 0.7703 (pt0) cc_final: 0.7225 (pt0) REVERT: C 101 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: C 123 GLN cc_start: 0.9090 (tp40) cc_final: 0.8852 (tp40) REVERT: E 79 ASP cc_start: 0.7979 (p0) cc_final: 0.7621 (p0) REVERT: E 137 ASP cc_start: 0.8358 (t0) cc_final: 0.8123 (t0) REVERT: E 144 ASP cc_start: 0.8957 (p0) cc_final: 0.8692 (p0) REVERT: F 18 ASP cc_start: 0.8804 (t0) cc_final: 0.8422 (p0) REVERT: F 32 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7396 (mtt-85) REVERT: F 131 TYR cc_start: 0.7799 (p90) cc_final: 0.6967 (p90) REVERT: F 161 MET cc_start: 0.8946 (tpp) cc_final: 0.8673 (tpp) outliers start: 85 outliers final: 62 residues processed: 323 average time/residue: 0.2365 time to fit residues: 111.3489 Evaluate side-chains 324 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 251 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 34 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 199 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 30 optimal weight: 0.0970 chunk 89 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 70 optimal weight: 0.3980 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 overall best weight: 3.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN F 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12836 Z= 0.231 Angle : 0.588 10.269 17471 Z= 0.306 Chirality : 0.044 0.221 1940 Planarity : 0.004 0.040 2322 Dihedral : 4.579 19.807 1777 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 5.86 % Allowed : 28.21 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.21), residues: 1604 helix: 1.33 (0.30), residues: 290 sheet: -1.24 (0.26), residues: 400 loop : -1.82 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 37 HIS 0.004 0.001 HIS F 84 PHE 0.012 0.001 PHE F 53 TYR 0.026 0.002 TYR C 53 ARG 0.003 0.000 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 258 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8628 (m-80) REVERT: A 54 SER cc_start: 0.9048 (OUTLIER) cc_final: 0.8513 (p) REVERT: A 199 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8789 (t) REVERT: A 212 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8112 (tp30) REVERT: A 487 TRP cc_start: 0.8606 (OUTLIER) cc_final: 0.7413 (m-10) REVERT: A 492 GLU cc_start: 0.6186 (mm-30) cc_final: 0.5523 (mt-10) REVERT: A 809 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: B 6 ASN cc_start: 0.7355 (t0) cc_final: 0.7148 (t0) REVERT: B 9 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7956 (ttm-80) REVERT: B 67 THR cc_start: 0.8595 (m) cc_final: 0.8202 (t) REVERT: B 92 GLU cc_start: 0.7497 (tp30) cc_final: 0.7190 (tp30) REVERT: B 104 GLU cc_start: 0.8062 (mp0) cc_final: 0.7772 (mp0) REVERT: B 120 GLN cc_start: 0.8257 (mt0) cc_final: 0.7679 (mt0) REVERT: C 48 ILE cc_start: 0.9081 (mm) cc_final: 0.8803 (mt) REVERT: C 101 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: C 112 ARG cc_start: 0.8943 (mmt180) cc_final: 0.8416 (mmt180) REVERT: C 123 GLN cc_start: 0.9073 (tp40) cc_final: 0.8747 (tp40) REVERT: E 38 TYR cc_start: 0.8687 (t80) cc_final: 0.8119 (t80) REVERT: E 79 ASP cc_start: 0.7970 (p0) cc_final: 0.7570 (p0) REVERT: E 144 ASP cc_start: 0.8973 (p0) cc_final: 0.8610 (p0) REVERT: F 18 ASP cc_start: 0.8704 (t0) cc_final: 0.8352 (p0) REVERT: F 29 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7203 (ptmt) REVERT: F 131 TYR cc_start: 0.7752 (p90) cc_final: 0.6937 (p90) REVERT: F 161 MET cc_start: 0.8886 (tpp) cc_final: 0.8527 (tpp) outliers start: 79 outliers final: 55 residues processed: 316 average time/residue: 0.2218 time to fit residues: 103.4543 Evaluate side-chains 313 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 249 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 86 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 ASN ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN F 14 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12836 Z= 0.343 Angle : 0.646 9.959 17471 Z= 0.338 Chirality : 0.046 0.215 1940 Planarity : 0.004 0.040 2322 Dihedral : 4.802 19.924 1777 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 7.13 % Allowed : 27.32 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.72 (0.20), residues: 1604 helix: 1.12 (0.30), residues: 284 sheet: -1.38 (0.26), residues: 405 loop : -1.82 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 37 HIS 0.004 0.001 HIS F 84 PHE 0.011 0.002 PHE F 53 TYR 0.021 0.002 TYR C 101 ARG 0.004 0.000 ARG E 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 260 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8961 (mt) cc_final: 0.8713 (mm) REVERT: A 45 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.8738 (m-80) REVERT: A 54 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8521 (p) REVERT: A 199 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8703 (t) REVERT: A 487 TRP cc_start: 0.8689 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: A 492 GLU cc_start: 0.5929 (mm-30) cc_final: 0.5364 (mt-10) REVERT: A 759 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8433 (tpt-90) REVERT: A 809 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: B 9 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8261 (ttm-80) REVERT: B 67 THR cc_start: 0.8472 (m) cc_final: 0.8043 (t) REVERT: B 92 GLU cc_start: 0.7417 (tp30) cc_final: 0.7008 (tp30) REVERT: B 104 GLU cc_start: 0.8031 (mp0) cc_final: 0.7776 (mp0) REVERT: B 120 GLN cc_start: 0.8164 (mt0) cc_final: 0.7638 (mt0) REVERT: C 6 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7511 (t0) REVERT: C 48 ILE cc_start: 0.9117 (mm) cc_final: 0.7899 (mt) REVERT: C 54 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8365 (t) REVERT: C 101 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: E 4 LYS cc_start: 0.8821 (mmtp) cc_final: 0.8528 (mmtm) REVERT: E 27 LYS cc_start: 0.8568 (mtmm) cc_final: 0.7928 (mtpp) REVERT: E 79 ASP cc_start: 0.7950 (p0) cc_final: 0.7592 (p0) REVERT: E 144 ASP cc_start: 0.8971 (p0) cc_final: 0.8667 (p0) REVERT: F 18 ASP cc_start: 0.8745 (t0) cc_final: 0.8371 (p0) REVERT: F 29 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7359 (ptmt) REVERT: F 32 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7414 (mtt-85) REVERT: F 131 TYR cc_start: 0.7762 (p90) cc_final: 0.6891 (p90) outliers start: 96 outliers final: 69 residues processed: 331 average time/residue: 0.2367 time to fit residues: 115.3042 Evaluate side-chains 331 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 250 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN C 120 GLN E 156 ASN F 14 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12836 Z= 0.410 Angle : 0.690 9.651 17471 Z= 0.363 Chirality : 0.047 0.217 1940 Planarity : 0.005 0.053 2322 Dihedral : 5.044 20.239 1777 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 7.80 % Allowed : 27.17 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.90 (0.20), residues: 1604 helix: 0.91 (0.30), residues: 284 sheet: -1.49 (0.25), residues: 420 loop : -1.91 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 200 HIS 0.004 0.001 HIS A 523 PHE 0.015 0.002 PHE B 110 TYR 0.031 0.002 TYR C 53 ARG 0.005 0.001 ARG E 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 259 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8531 (p) REVERT: A 199 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8703 (t) REVERT: A 487 TRP cc_start: 0.8761 (OUTLIER) cc_final: 0.7571 (m-10) REVERT: A 759 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8414 (tpt-90) REVERT: D 91 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7565 (tp40) REVERT: B 9 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8243 (ttm-80) REVERT: B 67 THR cc_start: 0.8513 (m) cc_final: 0.8108 (t) REVERT: B 92 GLU cc_start: 0.7650 (tp30) cc_final: 0.7360 (tp30) REVERT: B 104 GLU cc_start: 0.8094 (mp0) cc_final: 0.7837 (mp0) REVERT: B 120 GLN cc_start: 0.8267 (mt0) cc_final: 0.7682 (mt0) REVERT: C 54 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8495 (t) REVERT: C 101 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.8103 (m-80) REVERT: C 123 GLN cc_start: 0.9054 (tp40) cc_final: 0.8792 (tp40) REVERT: E 27 LYS cc_start: 0.8597 (mtmm) cc_final: 0.7913 (mtpp) REVERT: E 79 ASP cc_start: 0.7944 (p0) cc_final: 0.7615 (p0) REVERT: E 144 ASP cc_start: 0.8954 (p0) cc_final: 0.8646 (p0) REVERT: F 18 ASP cc_start: 0.8755 (t0) cc_final: 0.8373 (p0) REVERT: F 29 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7385 (ptmt) REVERT: F 32 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7393 (mtt-85) REVERT: F 106 GLN cc_start: 0.8614 (mm110) cc_final: 0.8146 (mm-40) REVERT: F 131 TYR cc_start: 0.7758 (p90) cc_final: 0.6847 (p90) outliers start: 105 outliers final: 83 residues processed: 335 average time/residue: 0.2340 time to fit residues: 114.7674 Evaluate side-chains 342 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 249 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 763 ASP Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 104 TYR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 ASN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12836 Z= 0.216 Angle : 0.618 9.722 17471 Z= 0.322 Chirality : 0.045 0.216 1940 Planarity : 0.004 0.063 2322 Dihedral : 4.656 19.656 1777 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 5.35 % Allowed : 29.70 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.70 (0.21), residues: 1604 helix: 0.97 (0.30), residues: 289 sheet: -1.31 (0.25), residues: 419 loop : -1.78 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 216 HIS 0.004 0.001 HIS F 84 PHE 0.016 0.001 PHE B 110 TYR 0.023 0.002 TYR F 191 ARG 0.005 0.000 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 264 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 VAL cc_start: 0.8962 (OUTLIER) cc_final: 0.8719 (t) REVERT: A 487 TRP cc_start: 0.8545 (OUTLIER) cc_final: 0.7351 (m-10) REVERT: D 108 ASP cc_start: 0.7948 (t0) cc_final: 0.7723 (t0) REVERT: B 9 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8301 (ttm-80) REVERT: B 20 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.8988 (m) REVERT: B 67 THR cc_start: 0.8674 (m) cc_final: 0.8280 (t) REVERT: B 92 GLU cc_start: 0.7494 (tp30) cc_final: 0.7007 (tp30) REVERT: B 104 GLU cc_start: 0.8008 (mp0) cc_final: 0.7754 (mp0) REVERT: B 110 PHE cc_start: 0.8339 (t80) cc_final: 0.7998 (t80) REVERT: B 120 GLN cc_start: 0.8294 (mt0) cc_final: 0.7759 (mt0) REVERT: C 6 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.7514 (t0) REVERT: C 48 ILE cc_start: 0.8404 (mm) cc_final: 0.8203 (mt) REVERT: C 53 TYR cc_start: 0.6890 (p90) cc_final: 0.6671 (p90) REVERT: C 54 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8243 (t) REVERT: C 101 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7830 (m-80) REVERT: C 112 ARG cc_start: 0.8983 (mmt180) cc_final: 0.8456 (mmt180) REVERT: C 123 GLN cc_start: 0.8885 (tp40) cc_final: 0.8580 (tp40) REVERT: E 27 LYS cc_start: 0.8557 (mtmm) cc_final: 0.7872 (mtpp) REVERT: E 79 ASP cc_start: 0.7916 (p0) cc_final: 0.7504 (p0) REVERT: E 144 ASP cc_start: 0.9018 (p0) cc_final: 0.8635 (p0) REVERT: E 159 MET cc_start: 0.8574 (tpt) cc_final: 0.7484 (tmm) REVERT: F 14 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8511 (t0) REVERT: F 18 ASP cc_start: 0.8671 (t0) cc_final: 0.8376 (p0) REVERT: F 29 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7170 (ptmt) REVERT: F 131 TYR cc_start: 0.7634 (p90) cc_final: 0.6875 (p90) REVERT: F 161 MET cc_start: 0.8928 (tpp) cc_final: 0.8563 (tpp) outliers start: 72 outliers final: 58 residues processed: 318 average time/residue: 0.2211 time to fit residues: 103.1124 Evaluate side-chains 320 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 253 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN E 156 ASN ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12836 Z= 0.346 Angle : 0.678 9.971 17471 Z= 0.354 Chirality : 0.046 0.214 1940 Planarity : 0.005 0.077 2322 Dihedral : 4.878 20.111 1777 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 5.72 % Allowed : 29.55 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.81 (0.21), residues: 1604 helix: 0.88 (0.31), residues: 290 sheet: -1.38 (0.25), residues: 419 loop : -1.87 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 216 HIS 0.004 0.001 HIS A 523 PHE 0.016 0.002 PHE B 110 TYR 0.024 0.002 TYR E 92 ARG 0.004 0.000 ARG E 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 256 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8975 (mt) cc_final: 0.8724 (mm) REVERT: A 199 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8703 (t) REVERT: A 487 TRP cc_start: 0.8684 (OUTLIER) cc_final: 0.7500 (m-10) REVERT: A 657 GLU cc_start: 0.8991 (pt0) cc_final: 0.8708 (pm20) REVERT: B 9 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8237 (ttm-80) REVERT: B 67 THR cc_start: 0.8526 (m) cc_final: 0.8130 (t) REVERT: B 92 GLU cc_start: 0.7552 (tp30) cc_final: 0.7077 (tp30) REVERT: B 120 GLN cc_start: 0.8331 (mt0) cc_final: 0.7804 (mt0) REVERT: C 53 TYR cc_start: 0.6891 (p90) cc_final: 0.6687 (p90) REVERT: C 54 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8249 (t) REVERT: C 91 GLN cc_start: 0.8010 (pp30) cc_final: 0.7345 (pt0) REVERT: C 101 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7954 (m-80) REVERT: C 112 ARG cc_start: 0.8956 (mmt180) cc_final: 0.8479 (mmt180) REVERT: C 123 GLN cc_start: 0.9106 (tp40) cc_final: 0.8859 (tp40) REVERT: E 27 LYS cc_start: 0.8647 (mtmm) cc_final: 0.7910 (mtpp) REVERT: E 79 ASP cc_start: 0.7945 (p0) cc_final: 0.7577 (p0) REVERT: E 92 TYR cc_start: 0.8417 (t80) cc_final: 0.7431 (m-80) REVERT: E 144 ASP cc_start: 0.8991 (p0) cc_final: 0.8675 (p0) REVERT: E 159 MET cc_start: 0.8461 (tpt) cc_final: 0.7244 (ttt) REVERT: E 185 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.8244 (mmm-85) REVERT: F 14 ASN cc_start: 0.8770 (t0) cc_final: 0.8336 (t0) REVERT: F 18 ASP cc_start: 0.8621 (t0) cc_final: 0.8336 (p0) REVERT: F 29 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7238 (ptmt) REVERT: F 131 TYR cc_start: 0.7676 (p90) cc_final: 0.6859 (p90) outliers start: 77 outliers final: 67 residues processed: 314 average time/residue: 0.2344 time to fit residues: 108.0767 Evaluate side-chains 327 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 254 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain F residue 199 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 18 optimal weight: 30.0000 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 110 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 ASN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN ** F 36 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 = 0.3378 r_free = 0.3378 target = 0.100078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.089212 restraints weight = 34862.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.091394 restraints weight = 16696.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.092759 restraints weight = 9558.977| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12836 Z= 0.200 Angle : 0.612 10.309 17471 Z= 0.317 Chirality : 0.045 0.213 1940 Planarity : 0.004 0.077 2322 Dihedral : 4.526 18.818 1777 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 4.75 % Allowed : 30.44 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.64 (0.21), residues: 1604 helix: 1.04 (0.30), residues: 289 sheet: -1.25 (0.26), residues: 409 loop : -1.76 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 70 HIS 0.003 0.001 HIS F 84 PHE 0.020 0.001 PHE B 110 TYR 0.024 0.002 TYR E 92 ARG 0.006 0.000 ARG D 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2717.18 seconds wall clock time: 49 minutes 38.76 seconds (2978.76 seconds total)