Starting phenix.real_space_refine on Sun Nov 17 08:44:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j86_36061/11_2024/8j86_36061.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j86_36061/11_2024/8j86_36061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j86_36061/11_2024/8j86_36061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j86_36061/11_2024/8j86_36061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j86_36061/11_2024/8j86_36061.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j86_36061/11_2024/8j86_36061.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 35 5.49 5 S 67 5.16 5 C 8456 2.51 5 N 2225 2.21 5 O 2581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13367 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 8132 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 36, 'TRANS': 956} Chain breaks: 3 Chain: "B" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1686 Classifications: {'peptide': 209} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2830 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 8, 'TRANS': 341} Chain breaks: 10 Chain: "P" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 291 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" P DT P 17 " occ=0.04 ... (18 atoms not shown) pdb=" C6 DT P 17 " occ=0.04 residue: pdb=" P DT P 18 " occ=0.19 ... (18 atoms not shown) pdb=" C6 DT P 18 " occ=0.19 residue: pdb=" P DA P 19 " occ=0.49 ... (19 atoms not shown) pdb=" C4 DA P 19 " occ=0.49 residue: pdb=" P DA P 20 " occ=0.68 ... (19 atoms not shown) pdb=" C4 DA P 20 " occ=0.68 residue: pdb=" P DT T 1 " occ=0.32 ... (18 atoms not shown) pdb=" C6 DT T 1 " occ=0.32 residue: pdb=" P DT T 2 " occ=0.67 ... (18 atoms not shown) pdb=" C6 DT T 2 " occ=0.67 residue: pdb=" P DG T 3 " occ=0.68 ... (20 atoms not shown) pdb=" C4 DG T 3 " occ=0.68 residue: pdb=" P DA T 4 " occ=0.72 ... (19 atoms not shown) pdb=" C4 DA T 4 " occ=0.72 residue: pdb=" P DT T 5 " occ=0.49 ... (18 atoms not shown) pdb=" C6 DT T 5 " occ=0.49 residue: pdb=" P DC T 14 " occ=0.81 ... (17 atoms not shown) pdb=" C6 DC T 14 " occ=0.81 residue: pdb=" P DT T 15 " occ=0.33 ... (18 atoms not shown) pdb=" C6 DT T 15 " occ=0.33 residue: pdb=" P DC T 16 " occ=0.89 ... (17 atoms not shown) pdb=" C6 DC T 16 " occ=0.89 residue: pdb=" P DA T 17 " occ=0.92 ... (19 atoms not shown) pdb=" C4 DA T 17 " occ=0.92 Time building chain proxies: 8.11, per 1000 atoms: 0.61 Number of scatterers: 13367 At special positions: 0 Unit cell: (89.88, 113.4, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 67 16.00 P 35 15.00 O 2581 8.00 N 2225 7.00 C 8456 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.6 seconds 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 13 sheets defined 36.1% alpha, 10.8% beta 0 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.773A pdb=" N TYR A 47 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 48' Processing helix chain 'A' and resid 109 through 118 removed outlier: 3.540A pdb=" N PHE A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 240 through 254 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 448 through 474 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.738A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 514 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 621 through 639 removed outlier: 3.579A pdb=" N ARG A 628 " --> pdb=" O PRO A 624 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 652 Processing helix chain 'A' and resid 655 through 665 Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 680 through 700 Processing helix chain 'A' and resid 763 through 782 removed outlier: 3.610A pdb=" N SER A 767 " --> pdb=" O ASP A 763 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER A 780 " --> pdb=" O ARG A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 856 removed outlier: 3.558A pdb=" N ILE A 843 " --> pdb=" O HIS A 839 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 852 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU A 856 " --> pdb=" O GLU A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 876 removed outlier: 4.167A pdb=" N ILE A 866 " --> pdb=" O ASN A 862 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP A 875 " --> pdb=" O SER A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 881 removed outlier: 3.501A pdb=" N PHE A 880 " --> pdb=" O ARG A 877 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP A 881 " --> pdb=" O SER A 878 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 877 through 881' Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 969 through 983 removed outlier: 4.750A pdb=" N LYS A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 993 Processing helix chain 'B' and resid 19 through 38 removed outlier: 3.932A pdb=" N MET B 23 " --> pdb=" O TRP B 19 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TRP B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 3.507A pdb=" N LEU B 53 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS B 54 " --> pdb=" O ILE B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 54' Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 137 through 151 removed outlier: 3.757A pdb=" N LYS B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS B 151 " --> pdb=" O HIS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.666A pdb=" N ASN B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.656A pdb=" N LYS C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 42 removed outlier: 3.916A pdb=" N SER C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 147 through 158 removed outlier: 4.038A pdb=" N ILE C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 288 through 297 Processing helix chain 'C' and resid 315 through 324 removed outlier: 3.963A pdb=" N LEU C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 341 removed outlier: 3.537A pdb=" N SER C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 349 Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 364 through 374 Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 397 through 406 Processing helix chain 'C' and resid 406 through 424 removed outlier: 3.592A pdb=" N PHE C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 removed outlier: 7.949A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET A 1 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY A 123 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 153 " --> pdb=" O CYS A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.573A pdb=" N LEU A 90 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN A 56 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 72 through 73 removed outlier: 3.630A pdb=" N SER A 73 " --> pdb=" O VAL A 571 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 573 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 614 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL A 571 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE A 612 " --> pdb=" O VAL A 571 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL A 573 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER A 610 " --> pdb=" O VAL A 573 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 197 through 203 removed outlier: 3.616A pdb=" N THR A 186 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE A 164 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 259 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 303 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 359 Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 706 removed outlier: 6.092A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA A 793 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP A 549 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N PHE A 791 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 796 " --> pdb=" O MET A 809 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU A 798 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 807 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.267A pdb=" N VAL B 62 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TRP B 119 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL B 64 " --> pdb=" O TRP B 119 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 158 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLY B 179 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS B 157 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 85 through 89 Processing sheet with id=AB2, first strand: chain 'C' and resid 220 through 223 removed outlier: 7.245A pdb=" N ILE C 238 " --> pdb=" O GLU C 221 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 267 through 268 Processing sheet with id=AB4, first strand: chain 'C' and resid 301 through 303 411 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 4.45 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3889 1.34 - 1.45: 2293 1.45 - 1.57: 7355 1.57 - 1.69: 68 1.69 - 1.81: 102 Bond restraints: 13707 Sorted by residual: bond pdb=" C3' DA P 14 " pdb=" O3' DA P 14 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.74e+00 bond pdb=" N TYR C 60 " pdb=" CA TYR C 60 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.62e+00 bond pdb=" C PRO A 593 " pdb=" N PRO A 594 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.43e+00 bond pdb=" C3' DA T 12 " pdb=" O3' DA T 12 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" C3' DC T 14 " pdb=" O3' DC T 14 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.14e+00 ... (remaining 13702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 18196 1.44 - 2.87: 369 2.87 - 4.31: 66 4.31 - 5.75: 11 5.75 - 7.19: 5 Bond angle restraints: 18647 Sorted by residual: angle pdb=" C GLU A 339 " pdb=" CA GLU A 339 " pdb=" CB GLU A 339 " ideal model delta sigma weight residual 116.34 110.36 5.98 1.40e+00 5.10e-01 1.83e+01 angle pdb=" C PRO C 107 " pdb=" N ASP C 108 " pdb=" CA ASP C 108 " ideal model delta sigma weight residual 121.54 126.80 -5.26 1.91e+00 2.74e-01 7.58e+00 angle pdb=" N ASN B 83 " pdb=" CA ASN B 83 " pdb=" C ASN B 83 " ideal model delta sigma weight residual 114.56 111.19 3.37 1.27e+00 6.20e-01 7.04e+00 angle pdb=" C TYR C 60 " pdb=" CA TYR C 60 " pdb=" CB TYR C 60 " ideal model delta sigma weight residual 110.42 115.40 -4.98 1.99e+00 2.53e-01 6.26e+00 angle pdb=" C3' DA P 14 " pdb=" O3' DA P 14 " pdb=" P DG P 15 " ideal model delta sigma weight residual 120.20 123.85 -3.65 1.50e+00 4.44e-01 5.91e+00 ... (remaining 18642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 7930 35.64 - 71.29: 256 71.29 - 106.93: 14 106.93 - 142.57: 2 142.57 - 178.21: 2 Dihedral angle restraints: 8204 sinusoidal: 3616 harmonic: 4588 Sorted by residual: dihedral pdb=" CA SER C 196 " pdb=" C SER C 196 " pdb=" N ILE C 197 " pdb=" CA ILE C 197 " ideal model delta harmonic sigma weight residual 180.00 150.94 29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ASN A 109 " pdb=" C ASN A 109 " pdb=" N ILE A 110 " pdb=" CA ILE A 110 " ideal model delta harmonic sigma weight residual -180.00 -156.97 -23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA SER A 184 " pdb=" C SER A 184 " pdb=" N HIS A 185 " pdb=" CA HIS A 185 " ideal model delta harmonic sigma weight residual -180.00 -158.46 -21.54 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 8201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1771 0.056 - 0.112: 271 0.112 - 0.168: 29 0.168 - 0.224: 2 0.224 - 0.280: 1 Chirality restraints: 2074 Sorted by residual: chirality pdb=" CB ILE B 112 " pdb=" CA ILE B 112 " pdb=" CG1 ILE B 112 " pdb=" CG2 ILE B 112 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CG LEU A 546 " pdb=" CB LEU A 546 " pdb=" CD1 LEU A 546 " pdb=" CD2 LEU A 546 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU A 737 " pdb=" CB LEU A 737 " pdb=" CD1 LEU A 737 " pdb=" CD2 LEU A 737 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 2071 not shown) Planarity restraints: 2240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 45 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.63e+00 pdb=" N PRO B 46 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 46 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 46 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 592 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 593 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 593 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 593 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT P 17 " 0.021 2.00e-02 2.50e+03 1.01e-02 2.57e+00 pdb=" N1 DT P 17 " -0.021 2.00e-02 2.50e+03 pdb=" C2 DT P 17 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT P 17 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT P 17 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT P 17 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT P 17 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DT P 17 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT P 17 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT P 17 " -0.005 2.00e-02 2.50e+03 ... (remaining 2237 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 66 2.46 - 3.07: 8892 3.07 - 3.68: 20530 3.68 - 4.29: 29642 4.29 - 4.90: 48432 Nonbonded interactions: 107562 Sorted by model distance: nonbonded pdb="CA CA A1102 " pdb="CA CA A1103 " model vdw 1.849 1.980 nonbonded pdb=" O GLU A 879 " pdb=" OH TYR A 968 " model vdw 2.074 3.040 nonbonded pdb=" O ASN A 181 " pdb=" OH TYR A 271 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR A 332 " pdb=" OE1 GLU A 926 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR A 162 " pdb=" OE1 GLU A 476 " model vdw 2.259 3.040 ... (remaining 107557 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.99 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: 19.340 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 33.800 Find NCS groups from input model: 0.140 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 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 : 0.002 0.050 13707 Z= 0.153 Angle : 0.520 7.185 18647 Z= 0.282 Chirality : 0.041 0.280 2074 Planarity : 0.004 0.048 2240 Dihedral : 16.998 178.214 5236 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -1.41 (0.22), residues: 1518 helix: 1.07 (0.24), residues: 488 sheet: -0.52 (0.38), residues: 219 loop : -2.46 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 212 HIS 0.001 0.000 HIS A 36 PHE 0.020 0.001 PHE A 673 TYR 0.010 0.001 TYR A 658 ARG 0.003 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 SER cc_start: 0.8437 (m) cc_final: 0.8080 (m) REVERT: A 215 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7183 (tm-30) REVERT: A 374 ASP cc_start: 0.7372 (m-30) cc_final: 0.7166 (t0) REVERT: A 435 LYS cc_start: 0.7945 (ptpp) cc_final: 0.7192 (tptt) REVERT: A 525 LYS cc_start: 0.5422 (tptp) cc_final: 0.5173 (tptp) REVERT: A 539 LYS cc_start: 0.6881 (ttmt) cc_final: 0.6623 (ttmt) REVERT: A 668 TYR cc_start: 0.7115 (t80) cc_final: 0.6847 (t80) REVERT: A 844 LYS cc_start: 0.6512 (mtmt) cc_final: 0.5656 (ttmm) REVERT: A 909 TYR cc_start: 0.6059 (m-80) cc_final: 0.5778 (m-80) REVERT: A 993 PHE cc_start: 0.7632 (m-80) cc_final: 0.7387 (m-80) REVERT: C 243 LYS cc_start: 0.7844 (mttm) cc_final: 0.7488 (ttpp) REVERT: C 297 ILE cc_start: 0.6932 (mm) cc_final: 0.6705 (mp) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2906 time to fit residues: 114.2113 Evaluate side-chains 172 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.0040 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 0.0050 chunk 123 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.0670 chunk 91 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 overall best weight: 0.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 442 GLN A 897 HIS A 994 GLN B 120 ASN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13707 Z= 0.178 Angle : 0.593 7.265 18647 Z= 0.313 Chirality : 0.042 0.191 2074 Planarity : 0.005 0.065 2240 Dihedral : 16.415 179.714 2088 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 1.26 % Allowed : 9.21 % Favored : 89.53 % 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: -1.60 (0.22), residues: 1518 helix: 0.80 (0.24), residues: 503 sheet: -0.66 (0.37), residues: 222 loop : -2.56 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 119 HIS 0.008 0.001 HIS B 187 PHE 0.016 0.001 PHE C 272 TYR 0.028 0.001 TYR A 486 ARG 0.004 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.3919 (mpp) cc_final: 0.3597 (mpp) REVERT: A 374 ASP cc_start: 0.7389 (m-30) cc_final: 0.7089 (t0) REVERT: A 435 LYS cc_start: 0.7927 (ptpp) cc_final: 0.7098 (tptt) REVERT: A 525 LYS cc_start: 0.5583 (tptp) cc_final: 0.5181 (tptp) REVERT: A 539 LYS cc_start: 0.6885 (ttmt) cc_final: 0.6654 (ttmt) REVERT: A 620 GLU cc_start: 0.7322 (mp0) cc_final: 0.7047 (tt0) REVERT: A 668 TYR cc_start: 0.7123 (t80) cc_final: 0.6840 (t80) REVERT: A 741 TYR cc_start: 0.5873 (m-80) cc_final: 0.5078 (m-80) REVERT: A 844 LYS cc_start: 0.6588 (mtmt) cc_final: 0.5647 (ttmm) REVERT: A 899 ASN cc_start: 0.6307 (OUTLIER) cc_final: 0.6080 (p0) REVERT: C 243 LYS cc_start: 0.7878 (mttm) cc_final: 0.7514 (ttpp) outliers start: 18 outliers final: 11 residues processed: 209 average time/residue: 0.2558 time to fit residues: 78.9771 Evaluate side-chains 173 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 804 LYS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 392 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 39 optimal weight: 0.3980 chunk 142 optimal weight: 0.0270 chunk 154 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 141 optimal weight: 0.0370 chunk 48 optimal weight: 0.5980 chunk 114 optimal weight: 0.1980 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 181 ASN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13707 Z= 0.161 Angle : 0.562 7.775 18647 Z= 0.297 Chirality : 0.041 0.169 2074 Planarity : 0.004 0.058 2240 Dihedral : 16.370 179.891 2088 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 1.47 % Allowed : 13.19 % Favored : 85.35 % 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: -1.55 (0.22), residues: 1518 helix: 0.87 (0.24), residues: 499 sheet: -0.63 (0.38), residues: 219 loop : -2.53 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.006 0.001 HIS C 252 PHE 0.012 0.001 PHE A 328 TYR 0.017 0.001 TYR A 486 ARG 0.003 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ASP cc_start: 0.7388 (m-30) cc_final: 0.7156 (t0) REVERT: A 435 LYS cc_start: 0.7836 (ptpp) cc_final: 0.7054 (tptt) REVERT: A 525 LYS cc_start: 0.5700 (tptp) cc_final: 0.5273 (tptp) REVERT: A 539 LYS cc_start: 0.6869 (ttmt) cc_final: 0.6641 (ttmt) REVERT: A 620 GLU cc_start: 0.7251 (mp0) cc_final: 0.7029 (tt0) REVERT: A 668 TYR cc_start: 0.7089 (t80) cc_final: 0.6812 (t80) REVERT: A 741 TYR cc_start: 0.5742 (m-80) cc_final: 0.4999 (m-80) REVERT: C 100 SER cc_start: 0.7420 (m) cc_final: 0.7191 (t) REVERT: C 219 TYR cc_start: 0.6307 (t80) cc_final: 0.5617 (t80) REVERT: C 243 LYS cc_start: 0.7861 (mttm) cc_final: 0.7451 (tttp) REVERT: C 297 ILE cc_start: 0.6862 (mm) cc_final: 0.6635 (mp) outliers start: 21 outliers final: 15 residues processed: 196 average time/residue: 0.2522 time to fit residues: 73.2107 Evaluate side-chains 169 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 804 LYS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 392 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 151 optimal weight: 0.0980 chunk 135 optimal weight: 6.9990 chunk 40 optimal weight: 0.0470 chunk 126 optimal weight: 10.0000 overall best weight: 1.6284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS C 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13707 Z= 0.348 Angle : 0.689 8.256 18647 Z= 0.365 Chirality : 0.046 0.196 2074 Planarity : 0.005 0.059 2240 Dihedral : 16.630 179.180 2088 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 2.86 % Allowed : 15.21 % Favored : 81.93 % 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: -2.24 (0.21), residues: 1518 helix: 0.06 (0.23), residues: 511 sheet: -0.98 (0.37), residues: 221 loop : -2.82 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 8 HIS 0.009 0.001 HIS B 133 PHE 0.030 0.003 PHE A 328 TYR 0.022 0.002 TYR A 37 ARG 0.007 0.001 ARG A 849 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4169 (mpp) cc_final: 0.3761 (mpp) REVERT: A 106 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5032 (pm20) REVERT: A 374 ASP cc_start: 0.7464 (m-30) cc_final: 0.7073 (t0) REVERT: A 525 LYS cc_start: 0.5641 (tptp) cc_final: 0.5299 (tptp) REVERT: A 539 LYS cc_start: 0.7029 (ttmt) cc_final: 0.6784 (ttmt) REVERT: A 620 GLU cc_start: 0.7505 (mp0) cc_final: 0.7216 (tt0) REVERT: A 711 MET cc_start: 0.5447 (mmp) cc_final: 0.5179 (mmt) REVERT: A 833 ARG cc_start: 0.6653 (tpm170) cc_final: 0.6405 (tpm170) REVERT: C 100 SER cc_start: 0.7414 (m) cc_final: 0.7141 (t) REVERT: C 219 TYR cc_start: 0.6383 (t80) cc_final: 0.5583 (t80) REVERT: C 243 LYS cc_start: 0.7878 (mttm) cc_final: 0.7499 (ttpp) outliers start: 41 outliers final: 25 residues processed: 213 average time/residue: 0.2683 time to fit residues: 83.8169 Evaluate side-chains 190 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 804 LYS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 336 GLN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN B 133 HIS ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS C 252 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13707 Z= 0.205 Angle : 0.609 9.064 18647 Z= 0.323 Chirality : 0.043 0.231 2074 Planarity : 0.005 0.058 2240 Dihedral : 16.512 178.897 2088 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 2.37 % Allowed : 17.86 % Favored : 79.76 % 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: -2.02 (0.21), residues: 1518 helix: 0.36 (0.23), residues: 497 sheet: -0.89 (0.38), residues: 219 loop : -2.71 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.007 0.001 HIS C 252 PHE 0.016 0.001 PHE A 328 TYR 0.020 0.001 TYR A 909 ARG 0.010 0.000 ARG A 849 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4048 (mpp) cc_final: 0.3692 (mpp) REVERT: A 374 ASP cc_start: 0.7475 (m-30) cc_final: 0.7087 (t0) REVERT: A 525 LYS cc_start: 0.5533 (tptp) cc_final: 0.5127 (tptp) REVERT: A 539 LYS cc_start: 0.7002 (ttmt) cc_final: 0.6731 (ttmt) REVERT: A 620 GLU cc_start: 0.7467 (mp0) cc_final: 0.7120 (tt0) REVERT: A 833 ARG cc_start: 0.6558 (tpm170) cc_final: 0.6303 (tpm170) REVERT: A 853 MET cc_start: 0.6836 (ttp) cc_final: 0.6620 (mtm) REVERT: C 95 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.6234 (mtm) REVERT: C 100 SER cc_start: 0.7426 (m) cc_final: 0.7158 (t) REVERT: C 219 TYR cc_start: 0.6332 (t80) cc_final: 0.5519 (t80) REVERT: C 243 LYS cc_start: 0.7881 (mttm) cc_final: 0.7501 (ttpp) outliers start: 34 outliers final: 21 residues processed: 200 average time/residue: 0.2494 time to fit residues: 73.8295 Evaluate side-chains 183 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 6.9990 chunk 29 optimal weight: 0.1980 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 12 optimal weight: 0.0870 chunk 50 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 146 optimal weight: 0.0980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN C 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13707 Z= 0.175 Angle : 0.607 10.907 18647 Z= 0.318 Chirality : 0.042 0.199 2074 Planarity : 0.004 0.059 2240 Dihedral : 16.445 178.954 2088 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 2.09 % Allowed : 18.77 % Favored : 79.13 % 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: -1.89 (0.22), residues: 1518 helix: 0.42 (0.23), residues: 501 sheet: -0.78 (0.38), residues: 214 loop : -2.62 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.022 0.001 HIS B 187 PHE 0.022 0.001 PHE A 113 TYR 0.034 0.001 TYR A 909 ARG 0.009 0.000 ARG A 849 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4210 (mpp) cc_final: 0.3857 (mpp) REVERT: A 106 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.4815 (pm20) REVERT: A 250 GLN cc_start: 0.6926 (tt0) cc_final: 0.5881 (mm110) REVERT: A 374 ASP cc_start: 0.7427 (m-30) cc_final: 0.7098 (t0) REVERT: A 439 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6845 (p0) REVERT: A 471 GLU cc_start: 0.6050 (mt-10) cc_final: 0.5543 (mt-10) REVERT: A 525 LYS cc_start: 0.5395 (tptp) cc_final: 0.4931 (tptp) REVERT: A 539 LYS cc_start: 0.6956 (ttmt) cc_final: 0.6734 (ttmt) REVERT: A 620 GLU cc_start: 0.7441 (mp0) cc_final: 0.7118 (tt0) REVERT: A 853 MET cc_start: 0.6844 (ttp) cc_final: 0.6590 (mtp) REVERT: B 156 TYR cc_start: 0.5558 (t80) cc_final: 0.5356 (t80) REVERT: C 100 SER cc_start: 0.7498 (m) cc_final: 0.7226 (t) REVERT: C 200 ILE cc_start: 0.3926 (mp) cc_final: 0.3598 (mt) REVERT: C 243 LYS cc_start: 0.7907 (mttm) cc_final: 0.7446 (tttp) REVERT: C 322 LYS cc_start: 0.5654 (mmtm) cc_final: 0.5371 (tppt) outliers start: 30 outliers final: 18 residues processed: 187 average time/residue: 0.2376 time to fit residues: 67.1984 Evaluate side-chains 175 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13707 Z= 0.233 Angle : 0.628 12.193 18647 Z= 0.331 Chirality : 0.043 0.214 2074 Planarity : 0.005 0.061 2240 Dihedral : 16.494 178.810 2088 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 2.51 % Allowed : 19.19 % Favored : 78.30 % 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: -1.99 (0.22), residues: 1518 helix: 0.29 (0.23), residues: 501 sheet: -0.91 (0.37), residues: 227 loop : -2.65 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 136 HIS 0.007 0.001 HIS C 252 PHE 0.033 0.002 PHE A 113 TYR 0.016 0.002 TYR A 928 ARG 0.010 0.001 ARG A 849 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4202 (mpp) cc_final: 0.3921 (mpp) REVERT: A 106 GLU cc_start: 0.5958 (OUTLIER) cc_final: 0.4936 (pm20) REVERT: A 374 ASP cc_start: 0.7415 (m-30) cc_final: 0.7035 (t0) REVERT: A 439 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6853 (p0) REVERT: A 525 LYS cc_start: 0.5409 (tptp) cc_final: 0.5003 (tptp) REVERT: A 539 LYS cc_start: 0.6848 (ttmt) cc_final: 0.6608 (ttmt) REVERT: A 620 GLU cc_start: 0.7500 (mp0) cc_final: 0.7147 (tt0) REVERT: A 853 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.6552 (mtm) REVERT: A 869 LEU cc_start: 0.7542 (tp) cc_final: 0.7318 (tp) REVERT: A 926 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.4239 (pp20) REVERT: C 100 SER cc_start: 0.7467 (m) cc_final: 0.7217 (t) REVERT: C 200 ILE cc_start: 0.3721 (mp) cc_final: 0.3442 (mt) REVERT: C 219 TYR cc_start: 0.6292 (t80) cc_final: 0.5764 (t80) REVERT: C 243 LYS cc_start: 0.7919 (mttm) cc_final: 0.7580 (ttpp) REVERT: C 322 LYS cc_start: 0.5654 (mmtm) cc_final: 0.5369 (tppt) outliers start: 36 outliers final: 25 residues processed: 185 average time/residue: 0.2471 time to fit residues: 68.2772 Evaluate side-chains 182 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 909 TYR Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 0.3980 chunk 90 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 HIS B 120 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS C 164 ASN C 252 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13707 Z= 0.327 Angle : 0.709 11.669 18647 Z= 0.373 Chirality : 0.046 0.224 2074 Planarity : 0.005 0.060 2240 Dihedral : 16.658 178.062 2088 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.58 % Favored : 87.35 % Rotamer: Outliers : 2.86 % Allowed : 19.68 % Favored : 77.46 % 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: -2.38 (0.21), residues: 1518 helix: -0.14 (0.23), residues: 507 sheet: -1.16 (0.36), residues: 229 loop : -2.81 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 212 HIS 0.007 0.001 HIS B 133 PHE 0.046 0.002 PHE A 113 TYR 0.039 0.002 TYR A 909 ARG 0.011 0.001 ARG A 849 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4471 (mpp) cc_final: 0.4115 (mpp) REVERT: A 106 GLU cc_start: 0.5965 (OUTLIER) cc_final: 0.5049 (pm20) REVERT: A 374 ASP cc_start: 0.7499 (m-30) cc_final: 0.7093 (t0) REVERT: A 439 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.7038 (p0) REVERT: A 501 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7790 (mp) REVERT: A 525 LYS cc_start: 0.5557 (tptp) cc_final: 0.5187 (tptp) REVERT: A 620 GLU cc_start: 0.7660 (mp0) cc_final: 0.7272 (tt0) REVERT: A 833 ARG cc_start: 0.6647 (tpm170) cc_final: 0.6140 (tpm170) REVERT: A 891 MET cc_start: 0.7169 (mmm) cc_final: 0.6669 (mmm) REVERT: A 908 MET cc_start: 0.5044 (ppp) cc_final: 0.4640 (ppp) REVERT: A 926 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.4350 (pp20) REVERT: B 203 GLU cc_start: 0.6082 (tp30) cc_final: 0.5705 (tp30) REVERT: C 100 SER cc_start: 0.7372 (m) cc_final: 0.7117 (t) REVERT: C 200 ILE cc_start: 0.3610 (OUTLIER) cc_final: 0.3365 (mt) REVERT: C 219 TYR cc_start: 0.6329 (t80) cc_final: 0.5726 (t80) REVERT: C 243 LYS cc_start: 0.7949 (mttm) cc_final: 0.7486 (ttpp) outliers start: 41 outliers final: 27 residues processed: 194 average time/residue: 0.2416 time to fit residues: 69.2954 Evaluate side-chains 190 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 10.0000 chunk 141 optimal weight: 0.0070 chunk 144 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 127 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 HIS ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN B 187 HIS C 115 ASN C 164 ASN C 252 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13707 Z= 0.202 Angle : 0.649 11.392 18647 Z= 0.339 Chirality : 0.043 0.219 2074 Planarity : 0.004 0.061 2240 Dihedral : 16.512 177.816 2088 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.20 % Favored : 88.74 % Rotamer: Outliers : 2.37 % Allowed : 20.38 % Favored : 77.25 % 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: -2.22 (0.21), residues: 1518 helix: 0.08 (0.23), residues: 500 sheet: -0.95 (0.38), residues: 214 loop : -2.77 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 136 HIS 0.008 0.001 HIS C 252 PHE 0.032 0.001 PHE A 113 TYR 0.028 0.001 TYR A 668 ARG 0.013 0.001 ARG A 849 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4152 (mpp) cc_final: 0.3906 (mpp) REVERT: A 106 GLU cc_start: 0.5943 (OUTLIER) cc_final: 0.4935 (pm20) REVERT: A 250 GLN cc_start: 0.6924 (tt0) cc_final: 0.5830 (mm110) REVERT: A 374 ASP cc_start: 0.7468 (m-30) cc_final: 0.7110 (t0) REVERT: A 439 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6932 (p0) REVERT: A 525 LYS cc_start: 0.5411 (tptp) cc_final: 0.4959 (tptp) REVERT: A 620 GLU cc_start: 0.7522 (mp0) cc_final: 0.7085 (tt0) REVERT: A 868 ILE cc_start: 0.8252 (mt) cc_final: 0.7939 (tt) REVERT: A 908 MET cc_start: 0.4857 (ppp) cc_final: 0.4545 (ppp) REVERT: A 926 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.4085 (pp20) REVERT: C 100 SER cc_start: 0.7421 (m) cc_final: 0.7167 (t) REVERT: C 219 TYR cc_start: 0.6201 (t80) cc_final: 0.5665 (t80) REVERT: C 243 LYS cc_start: 0.7942 (mttm) cc_final: 0.7508 (tttp) REVERT: C 322 LYS cc_start: 0.5707 (mmtm) cc_final: 0.5423 (tppt) outliers start: 34 outliers final: 24 residues processed: 188 average time/residue: 0.2375 time to fit residues: 66.9485 Evaluate side-chains 182 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN C 164 ASN C 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13707 Z= 0.244 Angle : 0.657 10.259 18647 Z= 0.346 Chirality : 0.044 0.236 2074 Planarity : 0.005 0.062 2240 Dihedral : 16.524 177.910 2088 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.06 % Favored : 87.88 % Rotamer: Outliers : 2.37 % Allowed : 20.52 % Favored : 77.11 % 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: -2.28 (0.21), residues: 1518 helix: -0.01 (0.23), residues: 508 sheet: -1.08 (0.37), residues: 215 loop : -2.77 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 136 HIS 0.008 0.001 HIS C 252 PHE 0.041 0.002 PHE A 113 TYR 0.033 0.002 TYR A 668 ARG 0.008 0.001 ARG A 634 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4280 (mpp) cc_final: 0.4007 (mpp) REVERT: A 100 GLN cc_start: 0.5910 (pm20) cc_final: 0.4673 (mp10) REVERT: A 106 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.4961 (pm20) REVERT: A 250 GLN cc_start: 0.7094 (tt0) cc_final: 0.5767 (mm110) REVERT: A 374 ASP cc_start: 0.7485 (m-30) cc_final: 0.7094 (t0) REVERT: A 439 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6965 (p0) REVERT: A 525 LYS cc_start: 0.5427 (tptp) cc_final: 0.4973 (tptp) REVERT: A 620 GLU cc_start: 0.7585 (mp0) cc_final: 0.7181 (tt0) REVERT: A 853 MET cc_start: 0.6993 (mtp) cc_final: 0.6669 (mtm) REVERT: A 908 MET cc_start: 0.4779 (ppp) cc_final: 0.4525 (ppp) REVERT: C 100 SER cc_start: 0.7482 (m) cc_final: 0.7250 (t) REVERT: C 219 TYR cc_start: 0.6232 (t80) cc_final: 0.5660 (t80) REVERT: C 243 LYS cc_start: 0.7955 (mttm) cc_final: 0.7508 (tttp) REVERT: C 322 LYS cc_start: 0.5687 (mmtm) cc_final: 0.5412 (tppt) outliers start: 34 outliers final: 24 residues processed: 180 average time/residue: 0.2447 time to fit residues: 66.4598 Evaluate side-chains 177 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 402 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.0470 chunk 38 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 128 optimal weight: 0.0040 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.9894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.222793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.184681 restraints weight = 16389.288| |-----------------------------------------------------------------------------| r_work (start): 0.4468 rms_B_bonded: 2.55 r_work: 0.4204 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4197 r_free = 0.4197 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4196 r_free = 0.4196 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13707 Z= 0.256 Angle : 0.677 12.407 18647 Z= 0.354 Chirality : 0.045 0.226 2074 Planarity : 0.005 0.062 2240 Dihedral : 16.552 177.683 2088 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.92 % Favored : 88.01 % Rotamer: Outliers : 2.09 % Allowed : 20.87 % Favored : 77.04 % 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: -2.34 (0.21), residues: 1518 helix: -0.01 (0.23), residues: 501 sheet: -1.23 (0.37), residues: 217 loop : -2.78 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 136 HIS 0.008 0.001 HIS C 252 PHE 0.042 0.002 PHE A 113 TYR 0.028 0.002 TYR A 668 ARG 0.008 0.001 ARG A 634 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3218.04 seconds wall clock time: 60 minutes 20.75 seconds (3620.75 seconds total)