Starting phenix.real_space_refine on Sun Mar 17 04:41:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7e_23710/03_2024/7m7e_23710.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7e_23710/03_2024/7m7e_23710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7e_23710/03_2024/7m7e_23710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7e_23710/03_2024/7m7e_23710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7e_23710/03_2024/7m7e_23710.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7e_23710/03_2024/7m7e_23710.pdb" } resolution = 3.2 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= 0.001 sd= 0.061 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 48 5.16 5 C 10371 2.51 5 N 3016 2.21 5 O 3242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16677 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 6771 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 861} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 6771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 6771 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 861} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 193} Chain breaks: 2 Chain: "D" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1596 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 2 Time building chain proxies: 8.61, per 1000 atoms: 0.52 Number of scatterers: 16677 At special positions: 0 Unit cell: (94.6, 117.7, 196.9, 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 48 16.00 O 3242 8.00 N 3016 7.00 C 10371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 203 " distance=2.04 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 109 " distance=2.03 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 216 " distance=2.03 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: 5.84 Conformation dependent library (CDL) restraints added in 3.1 seconds 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4024 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 23 sheets defined 33.6% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'B' and resid 9 through 15 removed outlier: 3.873A pdb=" N ARG B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG B 15 " --> pdb=" O GLU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 105 through 110 removed outlier: 3.891A pdb=" N PHE B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 120 through 137 removed outlier: 3.762A pdb=" N ARG B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 192 removed outlier: 4.144A pdb=" N GLY B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 221 Processing helix chain 'B' and resid 237 through 246 removed outlier: 3.593A pdb=" N GLN B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 285 Processing helix chain 'B' and resid 311 through 325 removed outlier: 3.989A pdb=" N GLN B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 356 removed outlier: 3.875A pdb=" N ILE B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 415 through 419 removed outlier: 4.227A pdb=" N SER B 418 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 419 " --> pdb=" O TRP B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 419' Processing helix chain 'B' and resid 482 through 497 Processing helix chain 'B' and resid 503 through 514 Processing helix chain 'B' and resid 528 through 541 removed outlier: 3.697A pdb=" N ALA B 532 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 583 Processing helix chain 'B' and resid 583 through 598 removed outlier: 3.711A pdb=" N ALA B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 601 No H-bonds generated for 'chain 'B' and resid 599 through 601' Processing helix chain 'B' and resid 604 through 610 Processing helix chain 'B' and resid 620 through 641 Proline residue: B 626 - end of helix Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 667 through 685 removed outlier: 3.809A pdb=" N SER B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 705 Processing helix chain 'B' and resid 728 through 740 Processing helix chain 'B' and resid 759 through 769 removed outlier: 3.737A pdb=" N ARG B 762 " --> pdb=" O GLN B 759 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B 765 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 808 Processing helix chain 'B' and resid 811 through 821 Processing helix chain 'B' and resid 836 through 845 Processing helix chain 'B' and resid 865 through 878 removed outlier: 3.698A pdb=" N PHE B 869 " --> pdb=" O ASP B 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.558A pdb=" N VAL A 9 " --> pdb=" O ASP A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 32 removed outlier: 3.566A pdb=" N LEU A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.892A pdb=" N PHE A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 Processing helix chain 'A' and resid 120 through 137 removed outlier: 3.762A pdb=" N ARG A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 192 removed outlier: 4.145A pdb=" N GLY A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 221 Processing helix chain 'A' and resid 237 through 246 removed outlier: 3.593A pdb=" N GLN A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 311 through 325 removed outlier: 3.989A pdb=" N GLN A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 removed outlier: 3.874A pdb=" N ILE A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 399 Processing helix chain 'A' and resid 415 through 419 removed outlier: 4.227A pdb=" N SER A 418 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A 419 " --> pdb=" O TRP A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 415 through 419' Processing helix chain 'A' and resid 482 through 497 Processing helix chain 'A' and resid 503 through 514 Processing helix chain 'A' and resid 528 through 541 removed outlier: 3.698A pdb=" N ALA A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 583 through 598 removed outlier: 3.711A pdb=" N ALA A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 601 No H-bonds generated for 'chain 'A' and resid 599 through 601' Processing helix chain 'A' and resid 604 through 610 Processing helix chain 'A' and resid 620 through 641 Proline residue: A 626 - end of helix Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 667 through 685 removed outlier: 3.807A pdb=" N SER A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 760 through 762 No H-bonds generated for 'chain 'A' and resid 760 through 762' Processing helix chain 'A' and resid 763 through 771 removed outlier: 4.165A pdb=" N LEU A 767 " --> pdb=" O VAL A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 808 Processing helix chain 'A' and resid 811 through 821 Processing helix chain 'A' and resid 836 through 845 Processing helix chain 'A' and resid 865 through 878 removed outlier: 3.876A pdb=" N PHE A 869 " --> pdb=" O ASP A 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 removed outlier: 4.121A pdb=" N THR C 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 4.126A pdb=" N VAL D 104 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 150 Processing helix chain 'D' and resid 205 through 212 removed outlier: 4.132A pdb=" N LYS D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 197 through 200 removed outlier: 3.967A pdb=" N SER B 39 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU B 277 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE B 37 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA B 291 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY B 295 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 371 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU B 368 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AA3, first strand: chain 'B' and resid 400 through 401 Processing sheet with id=AA4, first strand: chain 'B' and resid 474 through 480 Processing sheet with id=AA5, first strand: chain 'B' and resid 782 through 783 removed outlier: 7.071A pdb=" N ALA B 647 " --> pdb=" O THR B 782 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 561 " --> pdb=" O PRO B 646 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 648 " --> pdb=" O VAL B 561 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 716 through 717 removed outlier: 4.307A pdb=" N ALA B 716 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 724 " --> pdb=" O ALA B 716 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N MET B 691 " --> pdb=" O ILE B 749 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 197 through 200 removed outlier: 3.967A pdb=" N SER A 39 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU A 277 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE A 37 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 291 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE A 454 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N SER A 296 " --> pdb=" O HIS A 452 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS A 452 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU A 298 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN A 450 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA A 335 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A 440 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 442 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 336 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU A 368 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA9, first strand: chain 'A' and resid 400 through 401 Processing sheet with id=AB1, first strand: chain 'A' and resid 474 through 480 Processing sheet with id=AB2, first strand: chain 'A' and resid 782 through 783 removed outlier: 7.071A pdb=" N ALA A 647 " --> pdb=" O THR A 782 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 561 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 648 " --> pdb=" O VAL A 561 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 716 through 717 removed outlier: 4.307A pdb=" N ALA A 716 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 724 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET A 691 " --> pdb=" O ILE A 749 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 5 through 9 Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 9 Processing sheet with id=AB6, first strand: chain 'C' and resid 13 through 14 removed outlier: 3.782A pdb=" N GLY C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 13 through 14 removed outlier: 4.226A pdb=" N TYR C 109 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 127 through 131 removed outlier: 3.756A pdb=" N GLY C 146 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TYR C 183 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 188 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AC1, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AC2, first strand: chain 'D' and resid 66 through 70 removed outlier: 6.548A pdb=" N TRP D 56 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR D 70 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU D 54 " --> pdb=" O TYR D 70 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 136 through 140 removed outlier: 3.629A pdb=" N LEU D 201 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS D 156 " --> pdb=" O SER D 199 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER D 199 " --> pdb=" O CYS D 156 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 182 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.553A pdb=" N TYR D 195 " --> pdb=" O ASN D 160 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 167 through 170 removed outlier: 4.159A pdb=" N LYS D 167 " --> pdb=" O THR D 219 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR D 219 " --> pdb=" O LYS D 167 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1926 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: 5.50 Time building geometry restraints manager: 6.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2893 1.28 - 1.41: 4059 1.41 - 1.55: 9937 1.55 - 1.68: 38 1.68 - 1.81: 78 Bond restraints: 17005 Sorted by residual: bond pdb=" C ARG B 440 " pdb=" O ARG B 440 " ideal model delta sigma weight residual 1.234 1.149 0.085 1.22e-02 6.72e+03 4.83e+01 bond pdb=" C GLU B 456 " pdb=" O GLU B 456 " ideal model delta sigma weight residual 1.235 1.177 0.058 1.14e-02 7.69e+03 2.61e+01 bond pdb=" CA ALA A 439 " pdb=" CB ALA A 439 " ideal model delta sigma weight residual 1.533 1.451 0.082 1.65e-02 3.67e+03 2.45e+01 bond pdb=" CA SER A 442 " pdb=" CB SER A 442 " ideal model delta sigma weight residual 1.532 1.443 0.089 1.82e-02 3.02e+03 2.37e+01 bond pdb=" CA ALA A 335 " pdb=" CB ALA A 335 " ideal model delta sigma weight residual 1.530 1.449 0.082 1.69e-02 3.50e+03 2.33e+01 ... (remaining 17000 not shown) Histogram of bond angle deviations from ideal: 86.14 - 95.75: 2 95.75 - 105.37: 419 105.37 - 114.98: 10128 114.98 - 124.59: 12170 124.59 - 134.20: 406 Bond angle restraints: 23125 Sorted by residual: angle pdb=" C ASP A 334 " pdb=" CA ASP A 334 " pdb=" CB ASP A 334 " ideal model delta sigma weight residual 109.55 87.82 21.73 1.68e+00 3.54e-01 1.67e+02 angle pdb=" C ARG B 790 " pdb=" CA ARG B 790 " pdb=" CB ARG B 790 " ideal model delta sigma weight residual 109.94 86.14 23.80 2.13e+00 2.20e-01 1.25e+02 angle pdb=" CA PHE B 265 " pdb=" CB PHE B 265 " pdb=" CG PHE B 265 " ideal model delta sigma weight residual 113.80 123.68 -9.88 1.00e+00 1.00e+00 9.77e+01 angle pdb=" N ALA A 16 " pdb=" CA ALA A 16 " pdb=" C ALA A 16 " ideal model delta sigma weight residual 113.88 104.06 9.82 1.23e+00 6.61e-01 6.37e+01 angle pdb=" C PHE B 265 " pdb=" CA PHE B 265 " pdb=" CB PHE B 265 " ideal model delta sigma weight residual 110.45 96.95 13.50 1.73e+00 3.34e-01 6.09e+01 ... (remaining 23120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 9198 17.71 - 35.41: 560 35.41 - 53.12: 241 53.12 - 70.83: 151 70.83 - 88.54: 25 Dihedral angle restraints: 10175 sinusoidal: 3884 harmonic: 6291 Sorted by residual: dihedral pdb=" C ARG B 790 " pdb=" N ARG B 790 " pdb=" CA ARG B 790 " pdb=" CB ARG B 790 " ideal model delta harmonic sigma weight residual -122.60 -89.88 -32.72 0 2.50e+00 1.60e-01 1.71e+02 dihedral pdb=" C ASP A 334 " pdb=" N ASP A 334 " pdb=" CA ASP A 334 " pdb=" CB ASP A 334 " ideal model delta harmonic sigma weight residual -122.60 -97.57 -25.03 0 2.50e+00 1.60e-01 1.00e+02 dihedral pdb=" N ARG B 790 " pdb=" C ARG B 790 " pdb=" CA ARG B 790 " pdb=" CB ARG B 790 " ideal model delta harmonic sigma weight residual 122.80 98.86 23.94 0 2.50e+00 1.60e-01 9.17e+01 ... (remaining 10172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2453 0.109 - 0.219: 122 0.219 - 0.328: 17 0.328 - 0.437: 8 0.437 - 0.547: 3 Chirality restraints: 2603 Sorted by residual: chirality pdb=" CA HIS A 339 " pdb=" N HIS A 339 " pdb=" C HIS A 339 " pdb=" CB HIS A 339 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.47e+00 chirality pdb=" CA ARG B 790 " pdb=" N ARG B 790 " pdb=" C ARG B 790 " pdb=" CB ARG B 790 " both_signs ideal model delta sigma weight residual False 2.51 3.05 -0.54 2.00e-01 2.50e+01 7.30e+00 chirality pdb=" CB VAL B 763 " pdb=" CA VAL B 763 " pdb=" CG1 VAL B 763 " pdb=" CG2 VAL B 763 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.91e+00 ... (remaining 2600 not shown) Planarity restraints: 3080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 800 " 0.833 9.50e-02 1.11e+02 3.73e-01 8.56e+01 pdb=" NE ARG A 800 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG A 800 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 800 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 800 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 798 " -0.031 2.00e-02 2.50e+03 6.32e-02 3.99e+01 pdb=" C ASP B 798 " 0.109 2.00e-02 2.50e+03 pdb=" O ASP B 798 " -0.043 2.00e-02 2.50e+03 pdb=" N ALA B 799 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 864 " -0.023 2.00e-02 2.50e+03 4.83e-02 2.34e+01 pdb=" C GLY A 864 " 0.084 2.00e-02 2.50e+03 pdb=" O GLY A 864 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP A 865 " -0.029 2.00e-02 2.50e+03 ... (remaining 3077 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 507 2.70 - 3.25: 15325 3.25 - 3.80: 24938 3.80 - 4.35: 32359 4.35 - 4.90: 55204 Nonbonded interactions: 128333 Sorted by model distance: nonbonded pdb=" O THR A 771 " pdb=" OG1 THR A 771 " model vdw 2.151 2.440 nonbonded pdb=" O THR B 771 " pdb=" OG1 THR B 771 " model vdw 2.151 2.440 nonbonded pdb=" O GLY C 111 " pdb=" OG SER D 64 " model vdw 2.213 2.440 nonbonded pdb=" NH2 ARG A 711 " pdb=" O VAL A 724 " model vdw 2.272 2.520 nonbonded pdb=" OG SER C 19 " pdb=" OD1 ASN C 88 " model vdw 2.272 2.440 ... (remaining 128328 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 'A' and (resid 4 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 911)) selection = (chain 'B' and (resid 4 through 439 or (resid 440 and (name N or name CA or name \ C or name O or name CB )) or resid 441 through 911)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.840 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: 8.720 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 42.740 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 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 : 0.006 0.089 17005 Z= 0.399 Angle : 1.086 23.800 23125 Z= 0.683 Chirality : 0.062 0.547 2603 Planarity : 0.011 0.373 3080 Dihedral : 16.734 88.536 6142 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 9.50 % Allowed : 3.94 % Favored : 86.57 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 3.42 % 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: -1.47 (0.17), residues: 2214 helix: -0.08 (0.20), residues: 702 sheet: -0.32 (0.26), residues: 410 loop : -1.85 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 430 HIS 0.017 0.001 HIS A 452 PHE 0.057 0.001 PHE B 265 TYR 0.051 0.002 TYR B 753 ARG 0.018 0.001 ARG A 764 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 236 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 VAL cc_start: 0.7764 (OUTLIER) cc_final: 0.7508 (t) REVERT: B 12 TYR cc_start: 0.8049 (m-10) cc_final: 0.7752 (m-80) REVERT: B 201 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6755 (m-30) REVERT: B 225 MET cc_start: 0.7856 (mtt) cc_final: 0.7514 (mtm) REVERT: B 265 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.6464 (p90) REVERT: B 409 GLU cc_start: 0.5691 (OUTLIER) cc_final: 0.5251 (pm20) REVERT: B 415 ASP cc_start: 0.6145 (OUTLIER) cc_final: 0.5726 (t0) REVERT: B 464 ARG cc_start: 0.2600 (OUTLIER) cc_final: 0.2258 (tpt90) REVERT: B 465 GLU cc_start: -0.3181 (OUTLIER) cc_final: -0.3414 (tp30) REVERT: B 557 ASP cc_start: 0.5082 (OUTLIER) cc_final: 0.4691 (t0) REVERT: B 764 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7386 (ttt90) REVERT: B 800 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7274 (mmt90) REVERT: A 11 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6444 (tp30) REVERT: A 60 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.5966 (mp0) REVERT: A 63 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7197 (mm-30) REVERT: A 100 ASP cc_start: 0.7536 (t0) cc_final: 0.7269 (t70) REVERT: A 201 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7245 (t0) REVERT: A 247 ARG cc_start: 0.8054 (mtt90) cc_final: 0.7616 (mtt180) REVERT: A 337 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7003 (mm-30) REVERT: A 415 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.6356 (m-30) REVERT: A 465 GLU cc_start: -0.3621 (OUTLIER) cc_final: -0.5378 (tm-30) REVERT: A 495 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6434 (mp0) REVERT: A 557 ASP cc_start: 0.5865 (OUTLIER) cc_final: 0.5438 (t0) REVERT: A 669 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: A 752 ASP cc_start: 0.7606 (t0) cc_final: 0.7406 (t0) REVERT: A 808 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6221 (pm20) REVERT: C 84 TYR cc_start: 0.7897 (m-80) cc_final: 0.7581 (m-80) REVERT: C 99 TYR cc_start: 0.7067 (m-80) cc_final: 0.6851 (m-80) outliers start: 164 outliers final: 27 residues processed: 358 average time/residue: 0.3974 time to fit residues: 192.0680 Evaluate side-chains 210 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 164 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 529 ARG Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 764 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 841 GLU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 53 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.6980 chunk 166 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 172 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 199 optimal weight: 20.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 GLN A 81 HIS ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17005 Z= 0.249 Angle : 0.607 7.747 23125 Z= 0.316 Chirality : 0.045 0.167 2603 Planarity : 0.005 0.062 3080 Dihedral : 8.722 102.762 2548 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.24 % Allowed : 10.02 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: -1.13 (0.17), residues: 2214 helix: 0.41 (0.20), residues: 727 sheet: -0.17 (0.26), residues: 409 loop : -1.83 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 430 HIS 0.004 0.001 HIS C 207 PHE 0.013 0.002 PHE C 31 TYR 0.021 0.002 TYR A 803 ARG 0.007 0.001 ARG B 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 164 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 TYR cc_start: 0.7851 (m-10) cc_final: 0.7563 (m-80) REVERT: B 225 MET cc_start: 0.8482 (mtt) cc_final: 0.8214 (mtm) REVERT: B 265 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7324 (p90) REVERT: B 337 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6601 (mm-30) REVERT: B 415 ASP cc_start: 0.6746 (OUTLIER) cc_final: 0.6323 (t0) REVERT: B 440 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5786 (mpp80) REVERT: B 464 ARG cc_start: 0.2948 (OUTLIER) cc_final: 0.2576 (mmt180) REVERT: B 465 GLU cc_start: -0.2944 (OUTLIER) cc_final: -0.3328 (tp30) REVERT: B 696 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6798 (mp) REVERT: B 800 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6617 (mmt90) REVERT: A 11 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6497 (tp30) REVERT: A 178 VAL cc_start: 0.8795 (m) cc_final: 0.8544 (t) REVERT: A 247 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7508 (mtt180) REVERT: A 281 GLU cc_start: 0.7612 (mp0) cc_final: 0.7102 (mm-30) REVERT: A 415 ASP cc_start: 0.6726 (OUTLIER) cc_final: 0.6392 (m-30) REVERT: A 495 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6563 (mm-30) REVERT: A 600 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7170 (ptm) REVERT: C 69 LYS cc_start: 0.5538 (tppt) cc_final: 0.5244 (tppt) outliers start: 56 outliers final: 19 residues processed: 207 average time/residue: 0.3425 time to fit residues: 101.1790 Evaluate side-chains 171 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 53 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 166 optimal weight: 0.0770 chunk 136 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 200 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 178 optimal weight: 0.5980 chunk 198 optimal weight: 0.2980 chunk 68 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17005 Z= 0.143 Angle : 0.495 8.043 23125 Z= 0.258 Chirality : 0.042 0.176 2603 Planarity : 0.004 0.052 3080 Dihedral : 6.207 82.066 2482 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.26 % Allowed : 12.10 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.18), residues: 2214 helix: 0.91 (0.20), residues: 729 sheet: 0.10 (0.26), residues: 400 loop : -1.72 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 639 HIS 0.003 0.000 HIS C 207 PHE 0.009 0.001 PHE C 31 TYR 0.015 0.001 TYR B 803 ARG 0.008 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 173 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 TYR cc_start: 0.7812 (m-10) cc_final: 0.7585 (m-80) REVERT: B 201 ASP cc_start: 0.7377 (t0) cc_final: 0.7073 (m-30) REVERT: B 225 MET cc_start: 0.8406 (mtt) cc_final: 0.8129 (mtm) REVERT: B 337 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6696 (mm-30) REVERT: B 415 ASP cc_start: 0.7181 (OUTLIER) cc_final: 0.6729 (t0) REVERT: B 464 ARG cc_start: 0.3286 (OUTLIER) cc_final: 0.2915 (mmt180) REVERT: B 465 GLU cc_start: -0.2826 (OUTLIER) cc_final: -0.3184 (tp30) REVERT: B 705 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5570 (tp) REVERT: B 800 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6554 (mmt90) REVERT: B 841 GLU cc_start: 0.6804 (tp30) cc_final: 0.6489 (mp0) REVERT: A 201 ASP cc_start: 0.7300 (t0) cc_final: 0.6438 (m-30) REVERT: A 247 ARG cc_start: 0.7866 (mtt90) cc_final: 0.7442 (mtt180) REVERT: A 281 GLU cc_start: 0.7651 (mp0) cc_final: 0.7148 (mm-30) REVERT: A 301 ASP cc_start: 0.7197 (m-30) cc_final: 0.6951 (m-30) REVERT: A 415 ASP cc_start: 0.6732 (OUTLIER) cc_final: 0.6456 (m-30) REVERT: A 495 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6655 (mm-30) REVERT: A 696 LEU cc_start: 0.4166 (OUTLIER) cc_final: 0.3872 (tt) REVERT: C 58 TYR cc_start: 0.8040 (m-80) cc_final: 0.7793 (m-80) REVERT: C 69 LYS cc_start: 0.5574 (tppt) cc_final: 0.5270 (tppt) REVERT: C 177 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7437 (mt) outliers start: 39 outliers final: 16 residues processed: 202 average time/residue: 0.3384 time to fit residues: 98.2182 Evaluate side-chains 166 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 53 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 103 optimal weight: 0.0050 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17005 Z= 0.187 Angle : 0.500 8.544 23125 Z= 0.260 Chirality : 0.042 0.166 2603 Planarity : 0.004 0.049 3080 Dihedral : 5.716 77.985 2471 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.43 % Allowed : 13.55 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2214 helix: 1.07 (0.20), residues: 728 sheet: 0.22 (0.26), residues: 398 loop : -1.62 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 639 HIS 0.003 0.001 HIS C 207 PHE 0.012 0.001 PHE D 92 TYR 0.013 0.001 TYR C 84 ARG 0.004 0.000 ARG B 711 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 153 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 TYR cc_start: 0.7834 (m-10) cc_final: 0.7597 (m-80) REVERT: B 201 ASP cc_start: 0.7555 (t0) cc_final: 0.7147 (m-30) REVERT: B 225 MET cc_start: 0.8481 (mtt) cc_final: 0.8248 (mtm) REVERT: B 337 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6830 (mm-30) REVERT: B 415 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7360 (t0) REVERT: B 434 GLU cc_start: 0.7669 (mp0) cc_final: 0.7431 (pm20) REVERT: B 464 ARG cc_start: 0.3165 (OUTLIER) cc_final: 0.2939 (mmt180) REVERT: B 465 GLU cc_start: -0.2804 (OUTLIER) cc_final: -0.3109 (tp30) REVERT: B 557 ASP cc_start: 0.7406 (t0) cc_final: 0.7183 (t0) REVERT: B 674 LEU cc_start: 0.6195 (mm) cc_final: 0.5899 (mm) REVERT: B 841 GLU cc_start: 0.6744 (tp30) cc_final: 0.6503 (mt-10) REVERT: A 247 ARG cc_start: 0.7853 (mtt90) cc_final: 0.7467 (mtt180) REVERT: A 281 GLU cc_start: 0.7614 (mp0) cc_final: 0.7239 (mm-30) REVERT: A 301 ASP cc_start: 0.7198 (m-30) cc_final: 0.6964 (m-30) REVERT: A 495 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6701 (mm-30) REVERT: C 69 LYS cc_start: 0.5534 (tppt) cc_final: 0.5212 (tppt) REVERT: C 84 TYR cc_start: 0.7434 (m-10) cc_final: 0.7028 (m-80) REVERT: C 122 SER cc_start: 0.5380 (p) cc_final: 0.4962 (t) outliers start: 42 outliers final: 25 residues processed: 185 average time/residue: 0.3503 time to fit residues: 93.2491 Evaluate side-chains 174 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 886 ASP Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 53 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 181 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 190 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17005 Z= 0.297 Angle : 0.573 9.276 23125 Z= 0.297 Chirality : 0.044 0.169 2603 Planarity : 0.005 0.069 3080 Dihedral : 5.666 81.586 2461 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.95 % Allowed : 13.95 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.18), residues: 2214 helix: 0.85 (0.20), residues: 733 sheet: 0.25 (0.26), residues: 395 loop : -1.62 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 639 HIS 0.004 0.001 HIS B 518 PHE 0.024 0.002 PHE A 152 TYR 0.013 0.002 TYR D 70 ARG 0.006 0.001 ARG B 711 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 155 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 TYR cc_start: 0.7956 (m-10) cc_final: 0.7738 (m-80) REVERT: B 201 ASP cc_start: 0.7740 (t0) cc_final: 0.7346 (m-30) REVERT: B 265 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7426 (p90) REVERT: B 337 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: B 464 ARG cc_start: 0.3688 (OUTLIER) cc_final: 0.3271 (mmt180) REVERT: B 465 GLU cc_start: -0.2346 (OUTLIER) cc_final: -0.2735 (tp30) REVERT: B 487 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6852 (mtt-85) REVERT: B 674 LEU cc_start: 0.6097 (mm) cc_final: 0.5769 (mm) REVERT: B 800 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6936 (mmt90) REVERT: B 841 GLU cc_start: 0.6523 (tp30) cc_final: 0.6300 (mt-10) REVERT: A 21 ARG cc_start: 0.6755 (mtm-85) cc_final: 0.6425 (ttp80) REVERT: A 247 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7572 (mtt180) REVERT: A 301 ASP cc_start: 0.7319 (m-30) cc_final: 0.7054 (m-30) REVERT: A 495 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6881 (mm-30) REVERT: A 578 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6805 (tm-30) REVERT: A 696 LEU cc_start: 0.4502 (OUTLIER) cc_final: 0.4266 (tt) REVERT: A 766 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6992 (mt-10) REVERT: A 777 ARG cc_start: 0.6706 (mtm110) cc_final: 0.6430 (mtp180) REVERT: C 69 LYS cc_start: 0.5667 (tppt) cc_final: 0.5318 (tppt) REVERT: C 122 SER cc_start: 0.5487 (p) cc_final: 0.5111 (t) REVERT: C 213 LYS cc_start: 0.7288 (mttt) cc_final: 0.6321 (tptt) outliers start: 51 outliers final: 32 residues processed: 196 average time/residue: 0.3496 time to fit residues: 97.4106 Evaluate side-chains 175 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 135 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 825 ASP Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 53 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 212 optimal weight: 20.0000 chunk 176 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17005 Z= 0.241 Angle : 0.534 9.672 23125 Z= 0.278 Chirality : 0.043 0.163 2603 Planarity : 0.004 0.048 3080 Dihedral : 5.065 58.056 2456 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.72 % Allowed : 14.88 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.18), residues: 2214 helix: 1.08 (0.20), residues: 719 sheet: 0.26 (0.26), residues: 412 loop : -1.53 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 639 HIS 0.004 0.001 HIS C 207 PHE 0.020 0.002 PHE A 152 TYR 0.012 0.001 TYR B 803 ARG 0.004 0.000 ARG A 711 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 140 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7326 (ttp80) REVERT: B 86 ASN cc_start: 0.6746 (t0) cc_final: 0.6285 (m-40) REVERT: B 201 ASP cc_start: 0.7721 (t0) cc_final: 0.7424 (m-30) REVERT: B 202 THR cc_start: 0.8296 (m) cc_final: 0.8077 (m) REVERT: B 337 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7058 (mm-30) REVERT: B 446 ILE cc_start: 0.8561 (tt) cc_final: 0.8290 (tt) REVERT: B 674 LEU cc_start: 0.6123 (mm) cc_final: 0.5677 (mt) REVERT: B 705 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7090 (tt) REVERT: B 800 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6886 (mmt90) REVERT: B 841 GLU cc_start: 0.6547 (tp30) cc_final: 0.6252 (mt-10) REVERT: A 79 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6225 (tt) REVERT: A 247 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7524 (mtt180) REVERT: A 301 ASP cc_start: 0.7257 (m-30) cc_final: 0.7028 (m-30) REVERT: A 355 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7631 (mp) REVERT: A 578 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6944 (tm-30) REVERT: A 600 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7718 (ptm) REVERT: A 696 LEU cc_start: 0.4509 (OUTLIER) cc_final: 0.4240 (tt) REVERT: A 777 ARG cc_start: 0.6598 (mtm110) cc_final: 0.6350 (mtp180) REVERT: C 36 MET cc_start: 0.8309 (mtt) cc_final: 0.8017 (mtt) REVERT: C 69 LYS cc_start: 0.5667 (tppt) cc_final: 0.5379 (tppt) REVERT: C 122 SER cc_start: 0.5539 (p) cc_final: 0.5187 (t) REVERT: C 213 LYS cc_start: 0.7271 (mttt) cc_final: 0.6306 (tptt) outliers start: 47 outliers final: 33 residues processed: 178 average time/residue: 0.3125 time to fit residues: 80.0425 Evaluate side-chains 174 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 ASP Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 886 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 53 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 179 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 HIS ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 HIS ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17005 Z= 0.212 Angle : 0.527 9.680 23125 Z= 0.272 Chirality : 0.043 0.161 2603 Planarity : 0.004 0.048 3080 Dihedral : 4.619 58.619 2447 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.78 % Allowed : 15.29 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2214 helix: 1.25 (0.20), residues: 713 sheet: 0.40 (0.26), residues: 407 loop : -1.50 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 639 HIS 0.004 0.001 HIS C 207 PHE 0.018 0.001 PHE A 152 TYR 0.014 0.001 TYR C 84 ARG 0.005 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 136 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7289 (ttp80) REVERT: B 86 ASN cc_start: 0.7058 (t0) cc_final: 0.6665 (m-40) REVERT: B 201 ASP cc_start: 0.7736 (t0) cc_final: 0.7414 (m-30) REVERT: B 202 THR cc_start: 0.8116 (m) cc_final: 0.7898 (m) REVERT: B 337 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7033 (mm-30) REVERT: B 446 ILE cc_start: 0.8591 (tt) cc_final: 0.8320 (tt) REVERT: B 487 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6701 (mtt-85) REVERT: B 674 LEU cc_start: 0.6059 (mm) cc_final: 0.5697 (mt) REVERT: B 841 GLU cc_start: 0.6548 (tp30) cc_final: 0.6229 (mt-10) REVERT: A 79 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6426 (tt) REVERT: A 201 ASP cc_start: 0.8128 (t0) cc_final: 0.7773 (t0) REVERT: A 247 ARG cc_start: 0.7836 (mtt90) cc_final: 0.7499 (mtt180) REVERT: A 355 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7616 (mp) REVERT: A 578 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6958 (tm-30) REVERT: A 600 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7742 (ptm) REVERT: A 696 LEU cc_start: 0.4518 (OUTLIER) cc_final: 0.4318 (tt) REVERT: C 36 MET cc_start: 0.8339 (mtt) cc_final: 0.8036 (mtt) REVERT: C 69 LYS cc_start: 0.5674 (tppt) cc_final: 0.5314 (tppt) REVERT: C 122 SER cc_start: 0.5579 (p) cc_final: 0.5245 (t) REVERT: C 213 LYS cc_start: 0.7216 (mttt) cc_final: 0.6264 (tptt) outliers start: 48 outliers final: 33 residues processed: 175 average time/residue: 0.3351 time to fit residues: 84.5331 Evaluate side-chains 173 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 132 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 825 ASP Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 53 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.0370 chunk 134 optimal weight: 1.9990 chunk 144 optimal weight: 0.0980 chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 192 optimal weight: 0.1980 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17005 Z= 0.139 Angle : 0.480 9.373 23125 Z= 0.246 Chirality : 0.041 0.150 2603 Planarity : 0.004 0.051 3080 Dihedral : 4.243 57.713 2447 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.20 % Allowed : 15.98 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 2214 helix: 1.55 (0.20), residues: 713 sheet: 0.53 (0.27), residues: 396 loop : -1.37 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 55 HIS 0.003 0.000 HIS C 207 PHE 0.013 0.001 PHE A 152 TYR 0.010 0.001 TYR C 98 ARG 0.006 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 148 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7291 (ttp80) REVERT: B 25 GLN cc_start: 0.7055 (tt0) cc_final: 0.6778 (tt0) REVERT: B 86 ASN cc_start: 0.7011 (t0) cc_final: 0.6660 (p0) REVERT: B 337 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: B 440 ARG cc_start: 0.6582 (mpp80) cc_final: 0.6056 (mpp80) REVERT: B 446 ILE cc_start: 0.8504 (tt) cc_final: 0.8209 (tt) REVERT: B 487 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6561 (mtt-85) REVERT: B 674 LEU cc_start: 0.6132 (mm) cc_final: 0.5702 (mt) REVERT: B 705 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7063 (tt) REVERT: B 841 GLU cc_start: 0.6522 (tp30) cc_final: 0.6218 (mt-10) REVERT: A 79 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6485 (tt) REVERT: A 201 ASP cc_start: 0.8059 (t0) cc_final: 0.7738 (t0) REVERT: A 247 ARG cc_start: 0.7735 (mtt90) cc_final: 0.7383 (mtt180) REVERT: A 301 ASP cc_start: 0.7215 (m-30) cc_final: 0.6995 (m-30) REVERT: A 355 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7331 (mp) REVERT: A 600 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7698 (ptm) REVERT: A 696 LEU cc_start: 0.4590 (OUTLIER) cc_final: 0.4386 (tt) REVERT: C 36 MET cc_start: 0.8237 (mtt) cc_final: 0.7910 (mtt) REVERT: C 69 LYS cc_start: 0.5654 (tppt) cc_final: 0.5273 (tppt) REVERT: C 108 ASP cc_start: 0.8208 (t0) cc_final: 0.7998 (t0) REVERT: C 122 SER cc_start: 0.5922 (p) cc_final: 0.5578 (t) REVERT: C 213 LYS cc_start: 0.7187 (mttt) cc_final: 0.6286 (tptt) outliers start: 38 outliers final: 18 residues processed: 178 average time/residue: 0.3365 time to fit residues: 86.6217 Evaluate side-chains 159 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain C residue 22 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 86 optimal weight: 0.0980 chunk 155 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 178 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17005 Z= 0.198 Angle : 0.514 8.274 23125 Z= 0.264 Chirality : 0.042 0.158 2603 Planarity : 0.004 0.048 3080 Dihedral : 4.310 59.312 2444 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.08 % Allowed : 15.81 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.18), residues: 2214 helix: 1.54 (0.20), residues: 713 sheet: 0.55 (0.27), residues: 401 loop : -1.35 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 639 HIS 0.003 0.001 HIS C 207 PHE 0.018 0.001 PHE D 92 TYR 0.016 0.001 TYR C 84 ARG 0.006 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 133 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 GLN cc_start: 0.7063 (tt0) cc_final: 0.6799 (tt0) REVERT: B 86 ASN cc_start: 0.6983 (t0) cc_final: 0.6659 (p0) REVERT: B 337 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7002 (mm-30) REVERT: B 409 GLU cc_start: 0.7203 (pm20) cc_final: 0.6921 (pt0) REVERT: B 440 ARG cc_start: 0.6607 (mpp80) cc_final: 0.5987 (mpp80) REVERT: B 487 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6660 (mtt-85) REVERT: B 674 LEU cc_start: 0.6012 (mm) cc_final: 0.5575 (mt) REVERT: B 705 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7066 (tt) REVERT: B 841 GLU cc_start: 0.6519 (tp30) cc_final: 0.6217 (mt-10) REVERT: A 78 ARG cc_start: 0.8130 (tpt90) cc_final: 0.7885 (tpt90) REVERT: A 79 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6463 (tt) REVERT: A 201 ASP cc_start: 0.8149 (t0) cc_final: 0.7836 (t0) REVERT: A 247 ARG cc_start: 0.7822 (mtt90) cc_final: 0.7476 (mtt180) REVERT: A 301 ASP cc_start: 0.7246 (m-30) cc_final: 0.7032 (m-30) REVERT: A 355 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7662 (mp) REVERT: A 578 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6860 (tm-30) REVERT: A 600 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7579 (ptm) REVERT: A 696 LEU cc_start: 0.4720 (OUTLIER) cc_final: 0.4501 (tt) REVERT: C 36 MET cc_start: 0.8228 (mtt) cc_final: 0.7887 (mtt) REVERT: C 69 LYS cc_start: 0.5724 (tppt) cc_final: 0.5366 (tppt) REVERT: C 122 SER cc_start: 0.5962 (p) cc_final: 0.5627 (t) REVERT: C 213 LYS cc_start: 0.7211 (mttt) cc_final: 0.6304 (tptt) outliers start: 36 outliers final: 25 residues processed: 163 average time/residue: 0.3353 time to fit residues: 79.6550 Evaluate side-chains 164 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 886 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain C residue 22 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.0010 chunk 127 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 219 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 174 optimal weight: 0.0670 chunk 18 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17005 Z= 0.174 Angle : 0.503 9.011 23125 Z= 0.258 Chirality : 0.042 0.154 2603 Planarity : 0.004 0.047 3080 Dihedral : 4.212 58.325 2444 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.03 % Allowed : 15.98 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 2214 helix: 1.69 (0.20), residues: 707 sheet: 0.54 (0.27), residues: 392 loop : -1.31 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 55 HIS 0.004 0.001 HIS D 47 PHE 0.018 0.001 PHE C 31 TYR 0.012 0.001 TYR C 98 ARG 0.007 0.000 ARG B 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 GLN cc_start: 0.7095 (tt0) cc_final: 0.6808 (tt0) REVERT: B 86 ASN cc_start: 0.7022 (t0) cc_final: 0.6750 (p0) REVERT: B 337 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6954 (mm-30) REVERT: B 409 GLU cc_start: 0.7104 (pm20) cc_final: 0.6895 (pt0) REVERT: B 440 ARG cc_start: 0.6626 (mpp80) cc_final: 0.6030 (mpp80) REVERT: B 487 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6601 (mtt-85) REVERT: B 674 LEU cc_start: 0.6060 (mm) cc_final: 0.5653 (mt) REVERT: B 705 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7073 (tt) REVERT: B 841 GLU cc_start: 0.6433 (tp30) cc_final: 0.6160 (mt-10) REVERT: A 79 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6544 (tt) REVERT: A 201 ASP cc_start: 0.8112 (t0) cc_final: 0.7836 (t0) REVERT: A 247 ARG cc_start: 0.7815 (mtt90) cc_final: 0.7427 (mtt180) REVERT: A 301 ASP cc_start: 0.7210 (m-30) cc_final: 0.6996 (m-30) REVERT: A 355 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7482 (mp) REVERT: A 578 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6915 (tm-30) REVERT: A 600 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7723 (ptm) REVERT: A 696 LEU cc_start: 0.4731 (OUTLIER) cc_final: 0.4510 (tt) REVERT: C 36 MET cc_start: 0.8204 (mtt) cc_final: 0.7867 (mtt) REVERT: C 69 LYS cc_start: 0.5611 (tppt) cc_final: 0.5191 (tppt) REVERT: C 122 SER cc_start: 0.6017 (p) cc_final: 0.5299 (t) REVERT: C 124 LYS cc_start: 0.6878 (tptp) cc_final: 0.6653 (mttp) REVERT: C 213 LYS cc_start: 0.7215 (mttt) cc_final: 0.6320 (tptt) outliers start: 35 outliers final: 25 residues processed: 162 average time/residue: 0.3438 time to fit residues: 80.4975 Evaluate side-chains 161 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 128 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 886 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain C residue 22 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 174 optimal weight: 0.0060 chunk 73 optimal weight: 7.9990 chunk 179 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.0040 chunk 153 optimal weight: 0.7980 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 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 = 0.4414 r_free = 0.4414 target = 0.194880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.140045 restraints weight = 20705.391| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.24 r_work: 0.3738 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17005 Z= 0.159 Angle : 0.491 8.396 23125 Z= 0.253 Chirality : 0.041 0.150 2603 Planarity : 0.004 0.048 3080 Dihedral : 4.118 57.480 2444 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.08 % Allowed : 16.21 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.18), residues: 2214 helix: 1.79 (0.20), residues: 709 sheet: 0.60 (0.27), residues: 392 loop : -1.26 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 55 HIS 0.003 0.001 HIS C 207 PHE 0.015 0.001 PHE D 92 TYR 0.013 0.001 TYR C 84 ARG 0.007 0.000 ARG B 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3801.45 seconds wall clock time: 68 minutes 53.19 seconds (4133.19 seconds total)