Starting phenix.real_space_refine on Sun Mar 17 21:52:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd4_13906/03_2024/7qd4_13906.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd4_13906/03_2024/7qd4_13906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd4_13906/03_2024/7qd4_13906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd4_13906/03_2024/7qd4_13906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd4_13906/03_2024/7qd4_13906.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qd4_13906/03_2024/7qd4_13906.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.002 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: 5 Type Number sf(0) Gaussians P 216 5.49 5 S 46 5.16 5 C 11474 2.51 5 N 3400 2.21 5 O 3982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D GLU 419": "OE1" <-> "OE2" Residue "D TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19118 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7345 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 27, 'TRANS': 880} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1110 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "C" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1104 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "E" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1110 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "F" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1104 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "D" Number of atoms: 7345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7345 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 27, 'TRANS': 880} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 9.43, per 1000 atoms: 0.49 Number of scatterers: 19118 At special positions: 0 Unit cell: (108.006, 187.67, 152.434, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 216 15.00 O 3982 8.00 N 3400 7.00 C 11474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 8.71 Conformation dependent library (CDL) restraints added in 2.7 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3436 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 69.7% alpha, 2.2% beta 102 base pairs and 175 stacking pairs defined. Time for finding SS restraints: 7.25 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.736A pdb=" N THR A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 41 Processing helix chain 'A' and resid 45 through 61 removed outlier: 3.900A pdb=" N ARG A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.519A pdb=" N VAL A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.751A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 113 removed outlier: 4.254A pdb=" N LEU A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 removed outlier: 3.506A pdb=" N LYS A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.549A pdb=" N MET A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 184 removed outlier: 3.730A pdb=" N ILE A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 206 through 213 Processing helix chain 'A' and resid 219 through 237 Processing helix chain 'A' and resid 246 through 260 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 269 through 318 removed outlier: 3.924A pdb=" N GLN A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 343 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 355 through 370 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.864A pdb=" N ASN A 382 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.558A pdb=" N VAL A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 407 through 424 Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.917A pdb=" N TYR A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 471 Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.506A pdb=" N TYR A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 489' Processing helix chain 'A' and resid 494 through 499 removed outlier: 3.677A pdb=" N VAL A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 530 Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.344A pdb=" N ALA A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 Processing helix chain 'A' and resid 588 through 592 Processing helix chain 'A' and resid 602 through 618 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 633 through 645 removed outlier: 3.557A pdb=" N MET A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 664 removed outlier: 3.593A pdb=" N GLN A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 4.132A pdb=" N TRP A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 738 removed outlier: 4.285A pdb=" N VAL A 732 " --> pdb=" O ASP A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 766 removed outlier: 3.510A pdb=" N ALA A 761 " --> pdb=" O ASP A 757 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 762 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 823 removed outlier: 5.339A pdb=" N GLU A 812 " --> pdb=" O LYS A 808 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ASP A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 834 removed outlier: 4.004A pdb=" N LYS A 834 " --> pdb=" O LEU A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 841 through 866 removed outlier: 3.850A pdb=" N ALA A 845 " --> pdb=" O GLN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 891 Processing helix chain 'A' and resid 902 through 938 Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.713A pdb=" N THR D 28 " --> pdb=" O TRP D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 41 Processing helix chain 'D' and resid 45 through 61 removed outlier: 3.655A pdb=" N ARG D 49 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 85 removed outlier: 3.741A pdb=" N VAL D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 94 removed outlier: 3.712A pdb=" N VAL D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 113 removed outlier: 4.265A pdb=" N LEU D 101 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TRP D 102 " --> pdb=" O GLY D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 136 removed outlier: 4.433A pdb=" N GLN D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 153 removed outlier: 3.545A pdb=" N MET D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 184 removed outlier: 3.790A pdb=" N ILE D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 197 Processing helix chain 'D' and resid 206 through 213 Processing helix chain 'D' and resid 219 through 237 Processing helix chain 'D' and resid 246 through 260 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 269 through 318 removed outlier: 3.922A pdb=" N GLN D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 343 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 355 through 370 Processing helix chain 'D' and resid 377 through 382 removed outlier: 3.868A pdb=" N ASN D 382 " --> pdb=" O ASP D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 removed outlier: 3.544A pdb=" N VAL D 388 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'D' and resid 407 through 424 Processing helix chain 'D' and resid 441 through 446 removed outlier: 3.907A pdb=" N TYR D 446 " --> pdb=" O GLN D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 471 Processing helix chain 'D' and resid 484 through 489 removed outlier: 3.632A pdb=" N TYR D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 484 through 489' Processing helix chain 'D' and resid 494 through 499 removed outlier: 3.658A pdb=" N VAL D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 530 Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.358A pdb=" N ALA D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 587 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 602 through 618 Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 633 through 645 removed outlier: 3.558A pdb=" N MET D 645 " --> pdb=" O SER D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 664 removed outlier: 3.576A pdb=" N GLN D 664 " --> pdb=" O PHE D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 671 removed outlier: 4.198A pdb=" N TRP D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 738 removed outlier: 4.263A pdb=" N VAL D 732 " --> pdb=" O ASP D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 766 removed outlier: 3.659A pdb=" N ALA D 761 " --> pdb=" O ASP D 757 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 762 " --> pdb=" O GLN D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 823 removed outlier: 5.420A pdb=" N GLU D 812 " --> pdb=" O LYS D 808 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ASP D 813 " --> pdb=" O GLU D 809 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG D 816 " --> pdb=" O GLU D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 834 removed outlier: 4.001A pdb=" N LYS D 834 " --> pdb=" O LEU D 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 837 No H-bonds generated for 'chain 'D' and resid 835 through 837' Processing helix chain 'D' and resid 841 through 866 removed outlier: 3.843A pdb=" N ALA D 845 " --> pdb=" O GLN D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 891 Processing helix chain 'D' and resid 902 through 938 Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 403 Processing sheet with id=AA2, first strand: chain 'A' and resid 573 through 574 removed outlier: 7.067A pdb=" N ILE A 573 " --> pdb=" O ASN A 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 679 through 683 Processing sheet with id=AA4, first strand: chain 'A' and resid 748 through 750 removed outlier: 6.358A pdb=" N HIS A 748 " --> pdb=" O ALA A 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 401 through 403 Processing sheet with id=AA6, first strand: chain 'D' and resid 573 through 574 removed outlier: 7.068A pdb=" N ILE D 573 " --> pdb=" O ASN D 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 679 through 683 Processing sheet with id=AA8, first strand: chain 'D' and resid 748 through 750 removed outlier: 6.387A pdb=" N HIS D 748 " --> pdb=" O ALA D 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 883 hydrogen bonds defined for protein. 2607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 256 hydrogen bonds 512 hydrogen bond angles 0 basepair planarities 102 basepair parallelities 175 stacking parallelities Total time for adding SS restraints: 9.40 Time building geometry restraints manager: 9.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4435 1.34 - 1.46: 5382 1.46 - 1.58: 9611 1.58 - 1.70: 428 1.70 - 1.82: 90 Bond restraints: 19946 Sorted by residual: bond pdb=" CG1 ILE A 145 " pdb=" CD1 ILE A 145 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.09e+00 bond pdb=" N ARG A 426 " pdb=" CA ARG A 426 " ideal model delta sigma weight residual 1.459 1.480 -0.021 1.15e-02 7.56e+03 3.34e+00 bond pdb=" N GLU A 144 " pdb=" CA GLU A 144 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.23e-02 6.61e+03 3.18e+00 bond pdb=" CB ASN D 914 " pdb=" CG ASN D 914 " ideal model delta sigma weight residual 1.516 1.474 0.042 2.50e-02 1.60e+03 2.81e+00 bond pdb=" CB ASN A 914 " pdb=" CG ASN A 914 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.66e+00 ... (remaining 19941 not shown) Histogram of bond angle deviations from ideal: 96.14 - 103.72: 693 103.72 - 111.30: 8612 111.30 - 118.87: 7742 118.87 - 126.45: 9974 126.45 - 134.03: 867 Bond angle restraints: 27888 Sorted by residual: angle pdb=" N GLU A 144 " pdb=" CA GLU A 144 " pdb=" CB GLU A 144 " ideal model delta sigma weight residual 110.16 118.82 -8.66 1.48e+00 4.57e-01 3.42e+01 angle pdb=" CA MET A 153 " pdb=" C MET A 153 " pdb=" O MET A 153 " ideal model delta sigma weight residual 119.59 113.62 5.97 1.23e+00 6.61e-01 2.36e+01 angle pdb=" N GLU D 144 " pdb=" CA GLU D 144 " pdb=" CB GLU D 144 " ideal model delta sigma weight residual 110.30 117.39 -7.09 1.54e+00 4.22e-01 2.12e+01 angle pdb=" CA GLU A 144 " pdb=" CB GLU A 144 " pdb=" CG GLU A 144 " ideal model delta sigma weight residual 114.10 122.20 -8.10 2.00e+00 2.50e-01 1.64e+01 angle pdb=" C LYS D 425 " pdb=" N ARG D 426 " pdb=" CA ARG D 426 " ideal model delta sigma weight residual 122.08 127.51 -5.43 1.47e+00 4.63e-01 1.37e+01 ... (remaining 27883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 8854 17.61 - 35.23: 1432 35.23 - 52.84: 840 52.84 - 70.45: 226 70.45 - 88.06: 32 Dihedral angle restraints: 11384 sinusoidal: 6070 harmonic: 5314 Sorted by residual: dihedral pdb=" CA ARG D 942 " pdb=" C ARG D 942 " pdb=" N GLU D 943 " pdb=" CA GLU D 943 " ideal model delta harmonic sigma weight residual -180.00 -157.18 -22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ARG A 942 " pdb=" C ARG A 942 " pdb=" N GLU A 943 " pdb=" CA GLU A 943 " ideal model delta harmonic sigma weight residual -180.00 -158.20 -21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA VAL D 719 " pdb=" C VAL D 719 " pdb=" N LYS D 720 " pdb=" CA LYS D 720 " ideal model delta harmonic sigma weight residual 180.00 162.11 17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 11381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2462 0.053 - 0.105: 523 0.105 - 0.158: 93 0.158 - 0.210: 17 0.210 - 0.263: 3 Chirality restraints: 3098 Sorted by residual: chirality pdb=" CB ILE A 452 " pdb=" CA ILE A 452 " pdb=" CG1 ILE A 452 " pdb=" CG2 ILE A 452 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE D 452 " pdb=" CA ILE D 452 " pdb=" CG1 ILE D 452 " pdb=" CG2 ILE D 452 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA GLU A 419 " pdb=" N GLU A 419 " pdb=" C GLU A 419 " pdb=" CB GLU A 419 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 3095 not shown) Planarity restraints: 2804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 371 " 0.047 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO D 372 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 372 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 372 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 371 " -0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO A 372 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 372 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 372 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 426 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C ARG A 426 " -0.041 2.00e-02 2.50e+03 pdb=" O ARG A 426 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS A 427 " 0.014 2.00e-02 2.50e+03 ... (remaining 2801 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2515 2.76 - 3.30: 17100 3.30 - 3.83: 35764 3.83 - 4.37: 41648 4.37 - 4.90: 65199 Nonbonded interactions: 162226 Sorted by model distance: nonbonded pdb=" O MET A 614 " pdb=" OG1 THR A 618 " model vdw 2.227 2.440 nonbonded pdb=" O MET D 614 " pdb=" OG1 THR D 618 " model vdw 2.235 2.440 nonbonded pdb=" OP1 DC F1037 " pdb=" OH TYR D 47 " model vdw 2.285 2.440 nonbonded pdb=" O ILE A 145 " pdb=" OG1 THR A 149 " model vdw 2.299 2.440 nonbonded pdb=" OH TYR A 47 " pdb=" OP1 DC C1037 " model vdw 2.307 2.440 ... (remaining 162221 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' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.920 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: 18.240 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 59.060 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 19946 Z= 0.270 Angle : 0.823 10.974 27888 Z= 0.453 Chirality : 0.046 0.263 3098 Planarity : 0.006 0.070 2804 Dihedral : 22.058 88.065 7948 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.18), residues: 1780 helix: -0.35 (0.13), residues: 1164 sheet: -0.45 (0.84), residues: 44 loop : -0.51 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 670 HIS 0.005 0.001 HIS D 567 PHE 0.036 0.003 PHE A 128 TYR 0.031 0.002 TYR A 707 ARG 0.006 0.001 ARG D 872 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.893 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 1.6847 time to fit residues: 340.8401 Evaluate side-chains 130 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.0370 chunk 151 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 318 ASN A 368 GLN A 661 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 975 ASN D 318 ASN D 368 GLN D 661 GLN ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN D 914 ASN D 975 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19946 Z= 0.197 Angle : 0.528 7.997 27888 Z= 0.301 Chirality : 0.036 0.149 3098 Planarity : 0.004 0.052 2804 Dihedral : 24.768 88.694 4358 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.16 % Allowed : 8.65 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1780 helix: 1.23 (0.15), residues: 1164 sheet: -0.18 (0.87), residues: 44 loop : -0.27 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 670 HIS 0.003 0.001 HIS D 418 PHE 0.013 0.002 PHE D 892 TYR 0.015 0.001 TYR D 488 ARG 0.006 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.7006 (mt) REVERT: D 681 MET cc_start: 0.3778 (OUTLIER) cc_final: 0.3564 (ptp) outliers start: 18 outliers final: 6 residues processed: 151 average time/residue: 1.5282 time to fit residues: 256.9800 Evaluate side-chains 134 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 681 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 10.0000 chunk 56 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 196 optimal weight: 0.6980 chunk 162 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 318 ASN A 368 GLN A 661 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN D 368 GLN D 661 GLN ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 878 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19946 Z= 0.280 Angle : 0.546 7.518 27888 Z= 0.311 Chirality : 0.038 0.156 3098 Planarity : 0.004 0.051 2804 Dihedral : 24.895 86.175 4358 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.74 % Allowed : 10.52 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.20), residues: 1780 helix: 1.62 (0.15), residues: 1162 sheet: -0.04 (0.89), residues: 44 loop : -0.17 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 102 HIS 0.005 0.001 HIS A 418 PHE 0.019 0.002 PHE A 128 TYR 0.017 0.002 TYR D 634 ARG 0.005 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 8 residues processed: 146 average time/residue: 1.5547 time to fit residues: 252.3866 Evaluate side-chains 122 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 655 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.9980 chunk 136 optimal weight: 0.0370 chunk 94 optimal weight: 7.9990 chunk 20 optimal weight: 0.1980 chunk 86 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 193 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 chunk 173 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 603 GLN A 661 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19946 Z= 0.159 Angle : 0.489 8.143 27888 Z= 0.283 Chirality : 0.034 0.144 3098 Planarity : 0.003 0.042 2804 Dihedral : 24.657 86.730 4358 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.23 % Allowed : 13.03 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.20), residues: 1780 helix: 2.03 (0.15), residues: 1170 sheet: -0.14 (0.86), residues: 44 loop : -0.03 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 643 HIS 0.003 0.001 HIS D 525 PHE 0.019 0.001 PHE A 128 TYR 0.013 0.001 TYR A 927 ARG 0.007 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 139 average time/residue: 1.4862 time to fit residues: 230.9120 Evaluate side-chains 120 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 844 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 311 GLN A 368 GLN A 603 GLN A 661 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN D 368 GLN ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 19946 Z= 0.359 Angle : 0.580 7.089 27888 Z= 0.328 Chirality : 0.040 0.186 3098 Planarity : 0.004 0.052 2804 Dihedral : 24.917 85.145 4358 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.87 % Allowed : 13.61 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.66 (0.20), residues: 1780 helix: 1.78 (0.15), residues: 1164 sheet: -0.07 (0.89), residues: 44 loop : -0.15 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 356 HIS 0.005 0.001 HIS A 418 PHE 0.020 0.002 PHE A 965 TYR 0.038 0.002 TYR D 141 ARG 0.006 0.001 ARG D 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 906 GLN cc_start: 0.8198 (mm110) cc_final: 0.7982 (mm-40) outliers start: 29 outliers final: 10 residues processed: 139 average time/residue: 1.5656 time to fit residues: 242.0392 Evaluate side-chains 128 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 655 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 0.0980 chunk 101 optimal weight: 2.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 368 GLN A 603 GLN A 661 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN D 368 GLN D 878 ASN ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19946 Z= 0.202 Angle : 0.516 8.463 27888 Z= 0.296 Chirality : 0.036 0.141 3098 Planarity : 0.003 0.043 2804 Dihedral : 24.686 85.882 4358 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.68 % Allowed : 15.10 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.21), residues: 1780 helix: 2.03 (0.15), residues: 1172 sheet: 0.05 (0.88), residues: 44 loop : -0.03 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 102 HIS 0.003 0.001 HIS D 183 PHE 0.012 0.001 PHE A 965 TYR 0.013 0.001 TYR D 121 ARG 0.005 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7122 (mt) REVERT: D 60 ARG cc_start: 0.6637 (mtm-85) cc_final: 0.6024 (mtm180) REVERT: D 894 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7246 (mt0) outliers start: 26 outliers final: 12 residues processed: 146 average time/residue: 1.4925 time to fit residues: 242.6724 Evaluate side-chains 132 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 894 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 110 optimal weight: 0.3980 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 603 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19946 Z= 0.217 Angle : 0.523 7.577 27888 Z= 0.299 Chirality : 0.036 0.139 3098 Planarity : 0.003 0.043 2804 Dihedral : 24.657 86.583 4358 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.87 % Allowed : 15.74 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.21), residues: 1780 helix: 2.06 (0.15), residues: 1172 sheet: 0.09 (0.87), residues: 44 loop : 0.02 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 102 HIS 0.003 0.001 HIS D 418 PHE 0.024 0.002 PHE A 128 TYR 0.016 0.001 TYR D 141 ARG 0.004 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.7134 (mt) REVERT: A 894 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7224 (mt0) REVERT: D 156 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.6989 (mt) REVERT: D 894 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7269 (mt0) outliers start: 29 outliers final: 10 residues processed: 144 average time/residue: 1.5140 time to fit residues: 243.2002 Evaluate side-chains 136 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 894 GLN Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 894 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 131 optimal weight: 0.0470 chunk 95 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19946 Z= 0.182 Angle : 0.518 7.624 27888 Z= 0.296 Chirality : 0.035 0.139 3098 Planarity : 0.003 0.044 2804 Dihedral : 24.562 86.165 4358 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.48 % Allowed : 16.65 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.21), residues: 1780 helix: 2.14 (0.15), residues: 1180 sheet: 0.11 (0.86), residues: 44 loop : -0.04 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 495 HIS 0.003 0.001 HIS A 764 PHE 0.012 0.001 PHE A 760 TYR 0.014 0.001 TYR D 121 ARG 0.007 0.000 ARG D 470 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7129 (mt) REVERT: A 894 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7188 (mt0) REVERT: D 60 ARG cc_start: 0.6634 (mtm-85) cc_final: 0.6049 (mtm180) outliers start: 23 outliers final: 12 residues processed: 141 average time/residue: 1.3856 time to fit residues: 217.2413 Evaluate side-chains 132 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 894 GLN Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 367 LYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 655 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 5.9990 chunk 168 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 368 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 311 GLN D 368 GLN ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19946 Z= 0.292 Angle : 0.570 9.064 27888 Z= 0.321 Chirality : 0.038 0.157 3098 Planarity : 0.004 0.044 2804 Dihedral : 24.722 85.770 4358 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.68 % Allowed : 16.52 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.86 (0.21), residues: 1780 helix: 1.92 (0.15), residues: 1180 sheet: 0.14 (0.87), residues: 44 loop : -0.11 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 102 HIS 0.004 0.001 HIS D 183 PHE 0.031 0.002 PHE A 128 TYR 0.047 0.002 TYR D 141 ARG 0.007 0.000 ARG D 470 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 894 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7238 (mt0) REVERT: D 894 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7263 (mt0) outliers start: 26 outliers final: 15 residues processed: 136 average time/residue: 1.4975 time to fit residues: 228.0340 Evaluate side-chains 131 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 894 GLN Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 367 LYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 894 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 199 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 169 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19946 Z= 0.250 Angle : 0.554 8.182 27888 Z= 0.314 Chirality : 0.037 0.165 3098 Planarity : 0.004 0.043 2804 Dihedral : 24.709 86.878 4358 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.35 % Allowed : 17.16 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.85 (0.21), residues: 1780 helix: 1.92 (0.15), residues: 1178 sheet: 0.21 (0.87), residues: 44 loop : -0.11 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 495 HIS 0.003 0.001 HIS A 183 PHE 0.013 0.002 PHE D 965 TYR 0.017 0.001 TYR D 141 ARG 0.007 0.000 ARG D 470 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 894 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7125 (mp10) REVERT: D 894 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7245 (mt0) outliers start: 21 outliers final: 15 residues processed: 132 average time/residue: 1.4652 time to fit residues: 218.1348 Evaluate side-chains 131 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 894 GLN Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 367 LYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 894 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 158 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 139 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 368 GLN ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.218235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.178658 restraints weight = 22915.704| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 2.04 r_work: 0.3665 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19946 Z= 0.214 Angle : 0.547 8.252 27888 Z= 0.311 Chirality : 0.036 0.170 3098 Planarity : 0.004 0.046 2804 Dihedral : 24.705 87.020 4358 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.29 % Allowed : 17.48 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.91 (0.21), residues: 1780 helix: 1.97 (0.15), residues: 1176 sheet: 0.28 (0.88), residues: 44 loop : -0.11 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 102 HIS 0.003 0.001 HIS A 183 PHE 0.044 0.002 PHE A 128 TYR 0.015 0.001 TYR D 141 ARG 0.007 0.000 ARG D 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5474.31 seconds wall clock time: 101 minutes 5.08 seconds (6065.08 seconds total)