Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 13:59:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck1_16689/04_2023/8ck1_16689.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck1_16689/04_2023/8ck1_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_16689/04_2023/8ck1_16689.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck1_16689/04_2023/8ck1_16689.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck1_16689/04_2023/8ck1_16689.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck1_16689/04_2023/8ck1_16689.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 6.61, per 1000 atoms: 0.53 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: 5.16 Conformation dependent library (CDL) restraints added in 1.7 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: 1.26 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: 5.09 Time building geometry restraints manager: 5.56 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: 1.730 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: 6.760 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 34.830 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.020 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 328 average time/residue: 0.2537 time to fit residues: 119.1719 Evaluate side-chains 266 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 264 time to evaluate : 1.553 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4242 time to fit residues: 3.1709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 84 HIS F 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 12836 Z= 0.308 Angle : 0.620 8.647 17471 Z= 0.327 Chirality : 0.045 0.198 1940 Planarity : 0.004 0.052 2322 Dihedral : 4.727 20.407 1777 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer Outliers : 5.35 % 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: -1.94 (0.20), residues: 1604 helix: 0.81 (0.30), residues: 291 sheet: -1.63 (0.25), residues: 418 loop : -1.87 (0.20), residues: 895 *********************** 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 343 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 271 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 45 residues processed: 315 average time/residue: 0.2326 time to fit residues: 108.5887 Evaluate side-chains 290 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 245 time to evaluate : 1.456 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.1213 time to fit residues: 12.3007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 0.0970 chunk 119 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN A 774 GLN B 98 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN E 14 ASN E 173 GLN F 14 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 12836 Z= 0.267 Angle : 0.591 8.981 17471 Z= 0.311 Chirality : 0.044 0.207 1940 Planarity : 0.004 0.044 2322 Dihedral : 4.625 20.395 1777 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer Outliers : 3.56 % 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: -1.79 (0.20), residues: 1604 helix: 1.04 (0.30), residues: 294 sheet: -1.50 (0.26), residues: 400 loop : -1.84 (0.19), residues: 910 *********************** 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 309 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 261 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 24 residues processed: 298 average time/residue: 0.2465 time to fit residues: 109.7225 Evaluate side-chains 257 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 233 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1222 time to fit residues: 7.5503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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** ** 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** F 14 ASN F 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12836 Z= 0.206 Angle : 0.569 9.586 17471 Z= 0.298 Chirality : 0.044 0.209 1940 Planarity : 0.004 0.039 2322 Dihedral : 4.469 19.902 1777 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer Outliers : 3.41 % 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: -1.57 (0.21), residues: 1604 helix: 1.32 (0.30), residues: 290 sheet: -1.31 (0.26), residues: 400 loop : -1.75 (0.20), residues: 914 *********************** 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 302 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 256 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 25 residues processed: 286 average time/residue: 0.2523 time to fit residues: 104.6763 Evaluate side-chains 266 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 241 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1264 time to fit residues: 7.6041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 9.9990 chunk 86 optimal weight: 0.2980 chunk 2 optimal weight: 10.0000 chunk 113 optimal weight: 30.0000 chunk 63 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- 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** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN F 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 12836 Z= 0.277 Angle : 0.599 10.407 17471 Z= 0.313 Chirality : 0.045 0.219 1940 Planarity : 0.004 0.053 2322 Dihedral : 4.578 19.913 1777 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer Outliers : 2.30 % 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 (0.20), residues: 1604 helix: 1.23 (0.30), residues: 290 sheet: -1.36 (0.26), residues: 401 loop : -1.78 (0.20), residues: 913 *********************** 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 286 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 255 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 16 residues processed: 272 average time/residue: 0.2343 time to fit residues: 94.3618 Evaluate side-chains 251 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 235 time to evaluate : 1.588 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1204 time to fit residues: 5.7960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 98 GLN ** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 12836 Z= 0.241 Angle : 0.598 10.186 17471 Z= 0.313 Chirality : 0.045 0.268 1940 Planarity : 0.004 0.040 2322 Dihedral : 4.524 19.745 1777 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer Outliers : 2.15 % 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: 1.14 (0.30), residues: 290 sheet: -1.25 (0.26), residues: 400 loop : -1.74 (0.20), residues: 914 *********************** 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 274 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 245 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 10 residues processed: 263 average time/residue: 0.2521 time to fit residues: 97.7316 Evaluate side-chains 243 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 233 time to evaluate : 1.501 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1267 time to fit residues: 4.3006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 87 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 86 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 D 123 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN E 156 ASN F 36 GLN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.077 12836 Z= 0.433 Angle : 0.703 14.219 17471 Z= 0.369 Chirality : 0.048 0.361 1940 Planarity : 0.005 0.072 2322 Dihedral : 5.025 20.053 1777 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer Outliers : 3.04 % 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: -1.88 (0.20), residues: 1604 helix: 0.76 (0.30), residues: 290 sheet: -1.44 (0.26), residues: 401 loop : -1.88 (0.19), residues: 913 *********************** 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 287 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 246 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 23 residues processed: 271 average time/residue: 0.2349 time to fit residues: 94.9509 Evaluate side-chains 256 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 233 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1201 time to fit residues: 7.7998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 90 optimal weight: 0.2980 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN F 14 ASN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 12836 Z= 0.243 Angle : 0.628 14.633 17471 Z= 0.328 Chirality : 0.046 0.352 1940 Planarity : 0.004 0.060 2322 Dihedral : 4.753 20.628 1777 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer Outliers : 1.26 % 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: -1.65 (0.21), residues: 1604 helix: 0.97 (0.30), residues: 284 sheet: -1.28 (0.26), residues: 404 loop : -1.72 (0.20), residues: 916 *********************** 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 274 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 257 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 269 average time/residue: 0.2478 time to fit residues: 97.6680 Evaluate side-chains 257 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 249 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1173 time to fit residues: 3.7890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 141 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 111 optimal weight: 30.0000 chunk 43 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** C 120 GLN E 156 ASN F 14 ASN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 12836 Z= 0.302 Angle : 0.664 14.934 17471 Z= 0.346 Chirality : 0.046 0.357 1940 Planarity : 0.004 0.058 2322 Dihedral : 4.856 22.872 1777 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer Outliers : 0.89 % 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 (0.21), residues: 1604 helix: 0.89 (0.30), residues: 280 sheet: -1.25 (0.26), residues: 410 loop : -1.78 (0.20), residues: 914 *********************** 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 260 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 248 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 254 average time/residue: 0.2474 time to fit residues: 93.2831 Evaluate side-chains 248 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 242 time to evaluate : 1.432 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1201 time to fit residues: 3.3849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** ** B 98 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 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN F 14 ASN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 12836 Z= 0.358 Angle : 0.690 15.299 17471 Z= 0.362 Chirality : 0.047 0.359 1940 Planarity : 0.005 0.058 2322 Dihedral : 5.026 24.535 1777 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer Outliers : 0.45 % 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: -1.89 (0.20), residues: 1604 helix: 0.60 (0.30), residues: 286 sheet: -1.33 (0.26), residues: 405 loop : -1.88 (0.20), residues: 913 ********************** 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 246 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 240 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 243 average time/residue: 0.2458 time to fit residues: 88.4643 Evaluate side-chains 238 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 1.430 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1189 time to fit residues: 2.6433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 110 optimal weight: 40.0000 chunk 7 optimal weight: 2.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.100438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.089423 restraints weight = 34731.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.091607 restraints weight = 16741.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.092987 restraints weight = 9632.696| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12836 Z= 0.216 Angle : 0.645 14.765 17471 Z= 0.334 Chirality : 0.046 0.352 1940 Planarity : 0.004 0.055 2322 Dihedral : 4.709 24.947 1777 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer Outliers : 0.15 % 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: 0.87 (0.31), residues: 280 sheet: -1.21 (0.26), residues: 408 loop : -1.69 (0.20), residues: 916 =============================================================================== Job complete usr+sys time: 2575.21 seconds wall clock time: 47 minutes 32.21 seconds (2852.21 seconds total)