Starting phenix.real_space_refine on Thu Oct 29 08:29:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m76_63676/10_2026/9m76_63676.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m76_63676/10_2026/9m76_63676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m76_63676/10_2026/9m76_63676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m76_63676/10_2026/9m76_63676.map" model { file = "/net/cci-nas-00/data/ceres_data/9m76_63676/10_2026/9m76_63676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m76_63676/10_2026/9m76_63676.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.000 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: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 288 5.49 5 S 47 5.16 5 C 9627 2.51 5 N 3149 2.21 5 O 3707 1.98 5 H 14338 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31161 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1388 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1737 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1564 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1676 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1437 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1758 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1540 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 4556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 4556 Classifications: {'DNA': 144} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 143} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 4583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 4583 Classifications: {'DNA': 144} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 143} Chain: "A" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1833 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Chain: "K" Number of atoms: 9084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 9084 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 550} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' ZN': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24672 SG CYS K 302 72.741 64.461 36.396 1.00205.96 S ATOM 24721 SG CYS K 305 75.915 65.190 33.237 1.00213.94 S ATOM 24850 SG CYS K 313 74.012 62.212 33.570 1.00191.14 S ATOM 24920 SG CYS K 318 68.340 57.092 25.488 1.00192.66 S ATOM 24966 SG CYS K 321 71.389 56.407 24.378 1.00185.28 S ATOM 25307 SG CYS K 344 68.871 55.056 23.297 1.00191.92 S ATOM 25144 SG CYS K 333 58.481 58.032 33.666 1.00181.22 S ATOM 25181 SG CYS K 336 61.153 57.848 35.343 1.00178.30 S ATOM 25545 SG CYS K 360 60.615 54.182 32.853 1.00187.48 S ATOM 25584 SG CYS K 363 59.557 53.782 35.996 1.00182.94 S ATOM 30312 SG CYS K 739 24.773 96.365 73.794 1.00236.99 S ATOM 30624 SG CYS K 759 22.221 94.486 73.248 1.00234.38 S ATOM 30658 SG CYS K 762 22.523 95.743 76.298 1.00242.84 S ATOM 30074 SG CYS K 724 22.540 88.228 64.041 1.00190.72 S ATOM 30114 SG CYS K 727 21.692 86.338 62.193 1.00187.99 S ATOM 30386 SG CYS K 744 24.032 88.400 61.188 1.00199.26 S ATOM 30430 SG CYS K 747 19.710 89.362 61.450 1.00201.46 S Time building chain proxies: 4.51, per 1000 atoms: 0.14 Number of scatterers: 31161 At special positions: 0 Unit cell: (151.632, 120.285, 115.182, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 47 16.00 P 288 15.00 O 3707 8.00 N 3149 7.00 C 9627 6.00 H 14338 1.00 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: 2.26 Conformation dependent library (CDL) restraints added in 711.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 801 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 313 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 305 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 302 " pdb=" ZN K 802 " pdb="ZN ZN K 802 " - pdb=" ND1 HIS K 341 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 344 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 321 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 318 " pdb=" ZN K 803 " pdb="ZN ZN K 803 " - pdb=" SG CYS K 336 " pdb="ZN ZN K 803 " - pdb=" SG CYS K 360 " pdb="ZN ZN K 803 " - pdb=" SG CYS K 363 " pdb="ZN ZN K 803 " - pdb=" SG CYS K 333 " pdb=" ZN K 804 " pdb="ZN ZN K 804 " - pdb=" ND1 HIS K 741 " pdb="ZN ZN K 804 " - pdb=" SG CYS K 762 " pdb="ZN ZN K 804 " - pdb=" SG CYS K 759 " pdb="ZN ZN K 804 " - pdb=" SG CYS K 739 " pdb=" ZN K 805 " pdb="ZN ZN K 805 " - pdb=" SG CYS K 747 " pdb="ZN ZN K 805 " - pdb=" SG CYS K 744 " pdb="ZN ZN K 805 " - pdb=" SG CYS K 724 " pdb="ZN ZN K 805 " - pdb=" SG CYS K 727 " Number of angles added : 18 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2558 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 17 sheets defined 52.6% alpha, 10.9% beta 140 base pairs and 237 stacking pairs defined. Time for finding SS restraints: 5.17 Creating SS restraints... Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.502A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.721A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.094A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 122 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.137A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.545A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 4.003A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.337A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.527A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.360A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.503A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 removed outlier: 4.100A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.802A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.603A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 149 Processing helix chain 'K' and resid 273 through 277 removed outlier: 3.846A pdb=" N VAL K 277 " --> pdb=" O VAL K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 360 through 366 removed outlier: 3.770A pdb=" N ASP K 366 " --> pdb=" O GLU K 362 " (cutoff:3.500A) Processing helix chain 'K' and resid 366 through 383 removed outlier: 4.140A pdb=" N VAL K 370 " --> pdb=" O ASP K 366 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG K 378 " --> pdb=" O GLY K 374 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS K 381 " --> pdb=" O LEU K 377 " (cutoff:3.500A) Processing helix chain 'K' and resid 400 through 404 removed outlier: 4.165A pdb=" N VAL K 404 " --> pdb=" O MET K 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 432 through 439 removed outlier: 4.076A pdb=" N VAL K 436 " --> pdb=" O PHE K 432 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER K 437 " --> pdb=" O ARG K 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 502 through 510 Processing helix chain 'K' and resid 526 through 530 removed outlier: 3.520A pdb=" N GLY K 530 " --> pdb=" O TRP K 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 540 through 544 removed outlier: 3.709A pdb=" N LYS K 543 " --> pdb=" O LYS K 540 " (cutoff:3.500A) Processing helix chain 'K' and resid 591 through 602 Processing helix chain 'K' and resid 610 through 630 removed outlier: 3.590A pdb=" N ALA K 614 " --> pdb=" O GLY K 610 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG K 620 " --> pdb=" O ALA K 616 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS K 622 " --> pdb=" O ARG K 618 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU K 623 " --> pdb=" O GLU K 619 " (cutoff:3.500A) Processing helix chain 'K' and resid 677 through 687 Processing helix chain 'K' and resid 690 through 700 removed outlier: 4.129A pdb=" N GLU K 696 " --> pdb=" O LYS K 692 " (cutoff:3.500A) Processing helix chain 'K' and resid 701 through 703 No H-bonds generated for 'chain 'K' and resid 701 through 703' Processing helix chain 'K' and resid 709 through 722 Processing helix chain 'K' and resid 745 through 754 Processing helix chain 'K' and resid 775 through 786 Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.157A pdb=" N ARG B 45 " --> pdb=" O ILE A 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.875A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.840A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.845A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.128A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 128 through 129 removed outlier: 6.770A pdb=" N HIS K 185 " --> pdb=" O VAL K 157 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL K 159 " --> pdb=" O ILE K 183 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE K 183 " --> pdb=" O VAL K 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'K' and resid 265 through 271 removed outlier: 5.223A pdb=" N ASN K 267 " --> pdb=" O VAL K 259 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL K 259 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU K 255 " --> pdb=" O ILE K 271 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU K 254 " --> pdb=" O LYS K 246 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS K 246 " --> pdb=" O GLU K 254 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR K 256 " --> pdb=" O SER K 244 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP K 240 " --> pdb=" O VAL K 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 330 through 332 Processing sheet with id=AB6, first strand: chain 'K' and resid 449 through 450 removed outlier: 3.617A pdb=" N SER K 459 " --> pdb=" O HIS K 450 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY K 557 " --> pdb=" O VAL K 535 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG K 537 " --> pdb=" O TYR K 555 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N TYR K 555 " --> pdb=" O ARG K 537 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 470 through 471 removed outlier: 6.235A pdb=" N ARG K 581 " --> pdb=" O VAL K 561 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL K 561 " --> pdb=" O ARG K 581 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N MET K 429 " --> pdb=" O GLN K 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 734 through 736 553 hydrogen bonds defined for protein. 1593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 358 hydrogen bonds 716 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 8.76 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 14330 1.04 - 1.24: 1759 1.24 - 1.44: 6541 1.44 - 1.64: 9354 1.64 - 1.84: 68 Bond restraints: 32052 Sorted by residual: bond pdb=" P 5CM I -62 " pdb=" O5' 5CM I -62 " ideal model delta sigma weight residual 1.714 1.624 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C3' DG I -53 " pdb=" C2' DG I -53 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.84e+00 bond pdb=" C1' DC I -64 " pdb=" N1 DC I -64 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.81e+00 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.43e+00 bond pdb=" C3' DG J -22 " pdb=" C2' DG J -22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.43e+00 ... (remaining 32047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 54566 1.46 - 2.92: 3200 2.92 - 4.37: 211 4.37 - 5.83: 6 5.83 - 7.29: 1 Bond angle restraints: 57984 Sorted by residual: angle pdb=" O4' DG J -49 " pdb=" C4' DG J -49 " pdb=" C3' DG J -49 " ideal model delta sigma weight residual 106.00 103.61 2.39 6.00e-01 2.78e+00 1.59e+01 angle pdb=" N3 DT J 44 " pdb=" C4 DT J 44 " pdb=" O4 DT J 44 " ideal model delta sigma weight residual 119.90 122.27 -2.37 6.00e-01 2.78e+00 1.56e+01 angle pdb=" N3 DT I 15 " pdb=" C4 DT I 15 " pdb=" O4 DT I 15 " ideal model delta sigma weight residual 119.90 122.27 -2.37 6.00e-01 2.78e+00 1.55e+01 angle pdb=" N3 DT J 14 " pdb=" C4 DT J 14 " pdb=" O4 DT J 14 " ideal model delta sigma weight residual 119.90 122.26 -2.36 6.00e-01 2.78e+00 1.55e+01 angle pdb=" N3 DT I 71 " pdb=" C4 DT I 71 " pdb=" O4 DT I 71 " ideal model delta sigma weight residual 119.90 122.26 -2.36 6.00e-01 2.78e+00 1.54e+01 ... (remaining 57979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 10934 17.90 - 35.79: 1320 35.79 - 53.69: 1145 53.69 - 71.58: 436 71.58 - 89.48: 17 Dihedral angle restraints: 13852 sinusoidal: 9346 harmonic: 4506 Sorted by residual: dihedral pdb=" CA THR K 411 " pdb=" C THR K 411 " pdb=" N ILE K 412 " pdb=" CA ILE K 412 " ideal model delta harmonic sigma weight residual -180.00 -156.18 -23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ARG K 763 " pdb=" C ARG K 763 " pdb=" N TYR K 764 " pdb=" CA TYR K 764 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 13849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2294 0.059 - 0.118: 308 0.118 - 0.178: 191 0.178 - 0.237: 0 0.237 - 0.296: 1 Chirality restraints: 2794 Sorted by residual: chirality pdb=" C3' 5CM I -62 " pdb=" C4' 5CM I -62 " pdb=" O3' 5CM I -62 " pdb=" C2' 5CM I -62 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C3' DA J -12 " pdb=" C4' DA J -12 " pdb=" O3' DA J -12 " pdb=" C2' DA J -12 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" P DA I -67 " pdb=" OP1 DA I -67 " pdb=" OP2 DA I -67 " pdb=" O5' DA I -67 " both_signs ideal model delta sigma weight residual True 2.34 -2.50 -0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 2791 not shown) Planarity restraints: 3756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 5CM I -62 " -0.029 2.00e-02 2.50e+03 1.24e-02 4.22e+00 pdb=" N1 5CM I -62 " 0.003 2.00e-02 2.50e+03 pdb=" C2 5CM I -62 " 0.005 2.00e-02 2.50e+03 pdb=" O2 5CM I -62 " 0.007 2.00e-02 2.50e+03 pdb=" N3 5CM I -62 " 0.009 2.00e-02 2.50e+03 pdb=" C4 5CM I -62 " 0.010 2.00e-02 2.50e+03 pdb=" N4 5CM I -62 " -0.006 2.00e-02 2.50e+03 pdb=" C5 5CM I -62 " 0.013 2.00e-02 2.50e+03 pdb=" C6 5CM I -62 " 0.010 2.00e-02 2.50e+03 pdb="HN41 5CM I -62 " -0.012 2.00e-02 2.50e+03 pdb="HN42 5CM I -62 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 99 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO D 100 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 99 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO H 100 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " 0.022 5.00e-02 4.00e+02 ... (remaining 3753 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.76: 34 1.76 - 2.47: 17352 2.47 - 3.18: 90047 3.18 - 3.89: 121738 3.89 - 4.60: 196835 Nonbonded interactions: 426006 Sorted by model distance: nonbonded pdb=" HE1 HIS K 741 " pdb="ZN ZN K 804 " model vdw 1.048 1.408 nonbonded pdb=" OE1 GLU A 59 " pdb=" H GLU A 59 " model vdw 1.582 2.450 nonbonded pdb=" O CYS K 302 " pdb=" H LYS K 306 " model vdw 1.621 2.450 nonbonded pdb=" OD1 ASP K 471 " pdb=" H GLY K 473 " model vdw 1.623 2.450 nonbonded pdb=" OE1 GLU E 50 " pdb=" HE ARG F 39 " model vdw 1.629 2.450 ... (remaining 426001 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 134) selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 19 through 101) } ncs_group { reference = (chain 'C' and (resid 11 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 75 through 117 or (resid \ 118 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 119)) selection = (chain 'G' and (resid 11 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 14 through 119)) } ncs_group { reference = (chain 'D' and resid 27 through 122) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 39.000 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 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 : 0.009 0.571 17733 Z= 0.499 Angle : 1.011 39.370 25165 Z= 0.626 Chirality : 0.051 0.296 2794 Planarity : 0.004 0.047 2229 Dihedral : 22.949 89.479 7426 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.43 % Allowed : 1.90 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.23), residues: 1342 helix: 1.69 (0.21), residues: 673 sheet: -1.33 (0.49), residues: 95 loop : -0.25 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.009 0.001 TYR K 343 PHE 0.010 0.001 PHE K 273 TRP 0.008 0.001 TRP K 238 HIS 0.003 0.001 HIS K 741 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.43 (17714) covalent geometry : angle 0.71963 / 0.61 (25147) hydrogen bonds : bond 0.15896 / 11.04 ( 909) hydrogen bonds : angle 6.16279 / 4.39 ( 2309) metal coordination : bond 0.21975 / 11.73 ( 19) metal coordination : angle 26.57995 / 16.41 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 251 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8371 (mmm) cc_final: 0.8024 (mmm) REVERT: B 92 ARG cc_start: 0.7908 (ttp80) cc_final: 0.7611 (ttp80) REVERT: D 56 MET cc_start: 0.7374 (tpp) cc_final: 0.7022 (tpp) REVERT: G 24 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7717 (mm-40) REVERT: G 35 ARG cc_start: 0.8273 (mtm110) cc_final: 0.8053 (ttp-110) REVERT: G 114 VAL cc_start: 0.8228 (m) cc_final: 0.7997 (t) REVERT: H 102 GLU cc_start: 0.7463 (tt0) cc_final: 0.7169 (mm-30) REVERT: A 5 GLN cc_start: 0.6492 (tt0) cc_final: 0.5882 (tp40) REVERT: A 81 ASP cc_start: 0.8064 (m-30) cc_final: 0.7828 (t0) REVERT: K 302 CYS cc_start: 0.1425 (t) cc_final: 0.0899 (t) REVERT: K 578 TYR cc_start: 0.4998 (m-80) cc_final: 0.4531 (m-80) REVERT: K 589 PRO cc_start: 0.7972 (Cg_exo) cc_final: 0.7038 (Cg_endo) outliers start: 5 outliers final: 2 residues processed: 256 average time/residue: 0.4426 time to fit residues: 149.4048 Evaluate side-chains 141 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN C 112 GLN E 108 ASN F 25 ASN A 108 ASN K 200 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.114261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.089093 restraints weight = 192182.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.088743 restraints weight = 146893.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.089779 restraints weight = 104366.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.089738 restraints weight = 85336.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.089816 restraints weight = 82383.063| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 17733 Z= 0.337 Angle : 0.875 18.270 25165 Z= 0.500 Chirality : 0.050 0.190 2794 Planarity : 0.007 0.071 2229 Dihedral : 27.322 91.961 4696 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.09 % Allowed : 1.82 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.22), residues: 1342 helix: 0.98 (0.19), residues: 677 sheet: -2.01 (0.52), residues: 79 loop : -0.56 (0.23), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 431 TYR 0.029 0.002 TYR K 458 PHE 0.057 0.003 PHE G 25 TRP 0.019 0.002 TRP K 590 HIS 0.010 0.002 HIS K 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.34 (17714) covalent geometry : angle 0.84711 / 0.50 (25147) hydrogen bonds : bond 0.07889 / 5.40 ( 909) hydrogen bonds : angle 4.86700 / 3.48 ( 2309) metal coordination : bond 0.03948 / 2.57 ( 19) metal coordination : angle 8.21401 / 4.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8280 (mmm) cc_final: 0.7868 (mmm) REVERT: D 56 MET cc_start: 0.7549 (tpp) cc_final: 0.6791 (tpp) REVERT: D 80 TYR cc_start: 0.8315 (m-10) cc_final: 0.8056 (m-80) REVERT: G 24 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7726 (mm-40) REVERT: G 35 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7989 (ttp-110) REVERT: G 36 LYS cc_start: 0.8916 (ttpt) cc_final: 0.8592 (ttpp) REVERT: G 114 VAL cc_start: 0.8346 (m) cc_final: 0.8128 (p) REVERT: H 102 GLU cc_start: 0.7552 (tt0) cc_final: 0.7340 (mm-30) REVERT: K 354 SER cc_start: 0.5737 (m) cc_final: 0.5068 (p) REVERT: K 605 MET cc_start: 0.7999 (tpp) cc_final: 0.7767 (tpp) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.3783 time to fit residues: 75.6771 Evaluate side-chains 109 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [39, 143, 118, 94, 70, 98, 60, 138, 40, 63, 112] chunk 39 optimal weight: 20.0000 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 70 optimal weight: 50.0000 chunk 98 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.116207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.090926 restraints weight = 195166.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.091472 restraints weight = 139737.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.092297 restraints weight = 87733.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.092029 restraints weight = 77597.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.092229 restraints weight = 69583.331| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17733 Z= 0.174 Angle : 0.649 14.613 25165 Z= 0.401 Chirality : 0.043 0.176 2794 Planarity : 0.005 0.047 2229 Dihedral : 27.483 92.613 4696 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.09 % Allowed : 1.38 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.22), residues: 1342 helix: 1.39 (0.20), residues: 678 sheet: -1.85 (0.55), residues: 78 loop : -0.50 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 620 TYR 0.011 0.001 TYR B 72 PHE 0.021 0.002 PHE K 237 TRP 0.010 0.001 TRP K 238 HIS 0.007 0.001 HIS K 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.17 (17714) covalent geometry : angle 0.61927 / 0.40 (25147) hydrogen bonds : bond 0.05749 / 3.91 ( 909) hydrogen bonds : angle 4.22539 / 3.01 ( 2309) metal coordination : bond 0.01150 / 0.76 ( 19) metal coordination : angle 7.26453 / 4.38 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8022 (m-30) cc_final: 0.7790 (m-30) REVERT: B 84 MET cc_start: 0.8275 (mmm) cc_final: 0.7940 (mmm) REVERT: C 38 ASN cc_start: 0.6260 (t0) cc_final: 0.4964 (t0) REVERT: D 56 MET cc_start: 0.7525 (tpp) cc_final: 0.7138 (tpp) REVERT: G 24 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7665 (mm-40) REVERT: G 35 ARG cc_start: 0.8204 (mtm110) cc_final: 0.7984 (ttp-110) REVERT: G 36 LYS cc_start: 0.8874 (ttpt) cc_final: 0.8633 (ttpp) REVERT: G 38 ASN cc_start: 0.7852 (m110) cc_final: 0.7144 (m-40) REVERT: G 114 VAL cc_start: 0.8294 (m) cc_final: 0.8073 (p) REVERT: K 148 MET cc_start: 0.3873 (mtp) cc_final: 0.3523 (mtt) REVERT: K 589 PRO cc_start: 0.7863 (Cg_exo) cc_final: 0.6885 (Cg_endo) REVERT: K 605 MET cc_start: 0.7976 (tpp) cc_final: 0.7706 (tpp) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.3775 time to fit residues: 72.5548 Evaluate side-chains 115 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [61, 116, 59, 90, 63, 111, 28, 112, 42, 103, 110] chunk 61 optimal weight: 0.9980 chunk 116 optimal weight: 40.0000 chunk 59 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 GLN K 505 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.114238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.088068 restraints weight = 193028.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.089316 restraints weight = 150079.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.089102 restraints weight = 99884.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.089352 restraints weight = 90885.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.089418 restraints weight = 76373.021| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17733 Z= 0.253 Angle : 0.709 12.386 25165 Z= 0.425 Chirality : 0.044 0.162 2794 Planarity : 0.005 0.054 2229 Dihedral : 27.613 95.787 4696 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.09 % Allowed : 0.61 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.22), residues: 1342 helix: 1.25 (0.20), residues: 678 sheet: -1.77 (0.58), residues: 81 loop : -0.63 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.017 0.002 TYR K 547 PHE 0.017 0.002 PHE A 104 TRP 0.008 0.002 TRP K 127 HIS 0.010 0.001 HIS K 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.25 (17714) covalent geometry : angle 0.68888 / 0.42 (25147) hydrogen bonds : bond 0.06265 / 4.26 ( 909) hydrogen bonds : angle 4.35549 / 3.11 ( 2309) metal coordination : bond 0.01369 / 0.81 ( 19) metal coordination : angle 6.25375 / 3.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8309 (mmm) cc_final: 0.7980 (mmm) REVERT: C 38 ASN cc_start: 0.6389 (t0) cc_final: 0.5122 (t0) REVERT: D 56 MET cc_start: 0.7541 (tpp) cc_final: 0.7189 (tpp) REVERT: D 80 TYR cc_start: 0.8298 (m-10) cc_final: 0.8041 (m-80) REVERT: G 24 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7476 (mm-40) REVERT: G 35 ARG cc_start: 0.8194 (mtm110) cc_final: 0.7991 (ttp-110) REVERT: G 36 LYS cc_start: 0.8881 (ttpt) cc_final: 0.8654 (ttpp) REVERT: G 38 ASN cc_start: 0.7902 (m110) cc_final: 0.7237 (m-40) REVERT: G 114 VAL cc_start: 0.8371 (m) cc_final: 0.8163 (p) REVERT: K 148 MET cc_start: 0.3767 (mtp) cc_final: 0.3402 (mtt) REVERT: K 605 MET cc_start: 0.8143 (tpp) cc_final: 0.7821 (tpp) REVERT: K 681 SER cc_start: 0.4648 (m) cc_final: 0.4355 (p) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.3509 time to fit residues: 61.8045 Evaluate side-chains 108 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [89, 144, 69, 97, 45, 109, 88, 44, 28, 102, 136] chunk 89 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 69 optimal weight: 50.0000 chunk 97 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 88 optimal weight: 40.0000 chunk 44 optimal weight: 0.1980 chunk 28 optimal weight: 8.9990 chunk 102 optimal weight: 30.0000 chunk 136 optimal weight: 10.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.115139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.089156 restraints weight = 191520.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.089489 restraints weight = 140153.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.090289 restraints weight = 91029.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.090273 restraints weight = 79843.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.090361 restraints weight = 73081.069| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17733 Z= 0.178 Angle : 0.622 12.048 25165 Z= 0.387 Chirality : 0.041 0.161 2794 Planarity : 0.005 0.050 2229 Dihedral : 27.685 93.467 4696 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.09 % Allowed : 0.87 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.22), residues: 1342 helix: 1.53 (0.20), residues: 678 sheet: -1.80 (0.66), residues: 64 loop : -0.58 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 534 TYR 0.013 0.001 TYR K 547 PHE 0.019 0.001 PHE A 104 TRP 0.016 0.002 TRP K 527 HIS 0.005 0.001 HIS K 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.18 (17714) covalent geometry : angle 0.60424 / 0.39 (25147) hydrogen bonds : bond 0.05247 / 3.56 ( 909) hydrogen bonds : angle 4.02169 / 2.85 ( 2309) metal coordination : bond 0.01104 / 0.65 ( 19) metal coordination : angle 5.54504 / 3.56 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8314 (mmm) cc_final: 0.7895 (mmm) REVERT: C 38 ASN cc_start: 0.6291 (t0) cc_final: 0.5068 (t0) REVERT: D 56 MET cc_start: 0.7483 (tpp) cc_final: 0.7155 (tpp) REVERT: G 24 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7497 (mm-40) REVERT: G 35 ARG cc_start: 0.8224 (mtm110) cc_final: 0.7953 (ttp-110) REVERT: G 38 ASN cc_start: 0.7870 (m110) cc_final: 0.7067 (m-40) REVERT: G 114 VAL cc_start: 0.8354 (m) cc_final: 0.8142 (p) REVERT: K 148 MET cc_start: 0.3826 (mtp) cc_final: 0.3472 (mtt) REVERT: K 354 SER cc_start: 0.6092 (m) cc_final: 0.5500 (p) REVERT: K 605 MET cc_start: 0.8210 (tpp) cc_final: 0.7872 (tpp) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.3492 time to fit residues: 63.1124 Evaluate side-chains 108 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [48, 58, 11, 54, 119, 1, 133, 79, 22, 40, 70] chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 79 optimal weight: 50.0000 chunk 22 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 70 optimal weight: 50.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.114408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.087521 restraints weight = 192134.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.088092 restraints weight = 119844.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.088333 restraints weight = 85738.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.088424 restraints weight = 75379.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.088457 restraints weight = 68838.232| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17733 Z= 0.215 Angle : 0.648 10.292 25165 Z= 0.397 Chirality : 0.041 0.161 2794 Planarity : 0.005 0.055 2229 Dihedral : 27.726 93.028 4696 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.09 % Allowed : 0.87 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.22), residues: 1342 helix: 1.51 (0.20), residues: 672 sheet: -1.50 (0.66), residues: 67 loop : -0.76 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 534 TYR 0.016 0.002 TYR K 547 PHE 0.017 0.002 PHE A 104 TRP 0.006 0.001 TRP K 565 HIS 0.006 0.001 HIS K 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.21 (17714) covalent geometry : angle 0.63274 / 0.40 (25147) hydrogen bonds : bond 0.05617 / 3.84 ( 909) hydrogen bonds : angle 4.09016 / 2.90 ( 2309) metal coordination : bond 0.00701 / 0.46 ( 19) metal coordination : angle 5.18445 / 3.47 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8327 (mmm) cc_final: 0.7838 (mmm) REVERT: C 38 ASN cc_start: 0.6216 (t0) cc_final: 0.4934 (t0) REVERT: D 56 MET cc_start: 0.7449 (tpp) cc_final: 0.6831 (tpp) REVERT: D 80 TYR cc_start: 0.8270 (m-10) cc_final: 0.8025 (m-80) REVERT: G 24 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7536 (mm-40) REVERT: G 35 ARG cc_start: 0.8252 (mtm110) cc_final: 0.8005 (ttp-110) REVERT: G 38 ASN cc_start: 0.7823 (m110) cc_final: 0.7010 (m-40) REVERT: G 114 VAL cc_start: 0.8374 (m) cc_final: 0.8139 (p) REVERT: K 148 MET cc_start: 0.3899 (mtp) cc_final: 0.3539 (mtt) REVERT: K 289 MET cc_start: -0.1120 (tpt) cc_final: -0.1686 (tpt) REVERT: K 354 SER cc_start: 0.6081 (m) cc_final: 0.5501 (p) REVERT: K 429 MET cc_start: 0.6189 (mtp) cc_final: 0.5970 (mtp) REVERT: K 605 MET cc_start: 0.8269 (tpp) cc_final: 0.7933 (tpp) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.3251 time to fit residues: 58.3540 Evaluate side-chains 103 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [86, 52, 82, 143, 98, 125, 25, 13, 4, 117, 127] chunk 86 optimal weight: 50.0000 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 4 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.115605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.090267 restraints weight = 200317.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.090608 restraints weight = 145505.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.091618 restraints weight = 91586.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.091468 restraints weight = 75796.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.091579 restraints weight = 70051.474| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17733 Z= 0.159 Angle : 0.600 9.764 25165 Z= 0.374 Chirality : 0.040 0.155 2794 Planarity : 0.005 0.048 2229 Dihedral : 27.729 91.601 4696 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.09 % Allowed : 0.95 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.23), residues: 1342 helix: 1.70 (0.20), residues: 676 sheet: -1.90 (0.61), residues: 69 loop : -0.67 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.018 0.001 TYR F 72 PHE 0.017 0.001 PHE A 104 TRP 0.008 0.001 TRP K 590 HIS 0.006 0.001 HIS K 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.16 (17714) covalent geometry : angle 0.58557 / 0.37 (25147) hydrogen bonds : bond 0.04963 / 3.37 ( 909) hydrogen bonds : angle 3.85998 / 2.73 ( 2309) metal coordination : bond 0.00582 / 0.38 ( 19) metal coordination : angle 4.87436 / 3.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8252 (mmm) cc_final: 0.7801 (mmm) REVERT: D 56 MET cc_start: 0.7508 (tpp) cc_final: 0.6859 (tpp) REVERT: G 24 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7569 (mm-40) REVERT: G 35 ARG cc_start: 0.8196 (mtm110) cc_final: 0.7919 (ttp-110) REVERT: G 114 VAL cc_start: 0.8275 (m) cc_final: 0.8068 (p) REVERT: K 148 MET cc_start: 0.3834 (mtp) cc_final: 0.3473 (mtt) REVERT: K 289 MET cc_start: -0.1118 (tpt) cc_final: -0.1473 (tpt) REVERT: K 354 SER cc_start: 0.6082 (m) cc_final: 0.5466 (p) REVERT: K 429 MET cc_start: 0.6043 (mtp) cc_final: 0.5764 (mtp) REVERT: K 605 MET cc_start: 0.8227 (tpp) cc_final: 0.7873 (tpp) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.3098 time to fit residues: 56.9420 Evaluate side-chains 103 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [30, 22, 43, 3, 144, 41, 120, 86, 115, 69, 119] chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 120 optimal weight: 40.0000 chunk 86 optimal weight: 50.0000 chunk 115 optimal weight: 20.0000 chunk 69 optimal weight: 50.0000 chunk 119 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN K 505 ASN K 606 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.112444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.087152 restraints weight = 197016.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.087059 restraints weight = 197096.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.087962 restraints weight = 128338.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.087804 restraints weight = 113551.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.088041 restraints weight = 94645.380| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 17733 Z= 0.360 Angle : 0.806 11.733 25165 Z= 0.471 Chirality : 0.047 0.195 2794 Planarity : 0.007 0.059 2229 Dihedral : 28.013 91.126 4696 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.09 % Allowed : 0.87 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.22), residues: 1342 helix: 0.81 (0.20), residues: 674 sheet: -1.60 (0.63), residues: 66 loop : -1.10 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 39 TYR 0.025 0.003 TYR K 547 PHE 0.044 0.003 PHE A 104 TRP 0.014 0.002 TRP K 430 HIS 0.014 0.003 HIS K 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.36 (17714) covalent geometry : angle 0.79290 / 0.47 (25147) hydrogen bonds : bond 0.07598 / 5.26 ( 909) hydrogen bonds : angle 4.63123 / 3.30 ( 2309) metal coordination : bond 0.00798 / 0.55 ( 19) metal coordination : angle 5.44525 / 3.69 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 MET cc_start: 0.7484 (tpp) cc_final: 0.7168 (tpp) REVERT: G 24 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8172 (mm110) REVERT: G 35 ARG cc_start: 0.8269 (mtm110) cc_final: 0.8057 (ttp-110) REVERT: G 114 VAL cc_start: 0.8471 (m) cc_final: 0.8240 (p) REVERT: A 81 ASP cc_start: 0.7701 (t0) cc_final: 0.7472 (t0) REVERT: K 148 MET cc_start: 0.3840 (mtp) cc_final: 0.3479 (mtt) REVERT: K 289 MET cc_start: -0.1065 (tpt) cc_final: -0.1274 (tpt) REVERT: K 354 SER cc_start: 0.6040 (m) cc_final: 0.5444 (p) REVERT: K 401 MET cc_start: 0.6581 (mmt) cc_final: 0.6374 (mmm) REVERT: K 429 MET cc_start: 0.6337 (mtp) cc_final: 0.5983 (mtp) REVERT: K 605 MET cc_start: 0.8435 (tpp) cc_final: 0.8052 (tpp) outliers start: 1 outliers final: 1 residues processed: 116 average time/residue: 0.3386 time to fit residues: 55.3553 Evaluate side-chains 96 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [49, 59, 138, 14, 76, 55, 43, 128, 21, 86, 3] chunk 49 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 76 optimal weight: 50.0000 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 86 optimal weight: 50.0000 chunk 3 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.115360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.089684 restraints weight = 197384.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.089889 restraints weight = 156276.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.090702 restraints weight = 103691.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.090849 restraints weight = 91555.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.090988 restraints weight = 79866.275| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17733 Z= 0.149 Angle : 0.613 14.674 25165 Z= 0.377 Chirality : 0.041 0.153 2794 Planarity : 0.005 0.072 2229 Dihedral : 27.963 88.191 4696 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.22), residues: 1342 helix: 1.43 (0.20), residues: 679 sheet: -1.62 (0.57), residues: 82 loop : -0.80 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.016 0.002 TYR K 547 PHE 0.051 0.002 PHE G 25 TRP 0.011 0.001 TRP K 430 HIS 0.006 0.001 HIS K 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.15 (17714) covalent geometry : angle 0.59308 / 0.38 (25147) hydrogen bonds : bond 0.05146 / 3.48 ( 909) hydrogen bonds : angle 3.88994 / 2.75 ( 2309) metal coordination : bond 0.00817 / 0.47 ( 19) metal coordination : angle 5.89604 / 3.66 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 GLN cc_start: 0.7376 (mp10) cc_final: 0.6930 (mp10) REVERT: G 24 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7709 (mm-40) REVERT: G 35 ARG cc_start: 0.8160 (mtm110) cc_final: 0.7864 (ttp-110) REVERT: G 56 GLU cc_start: 0.7809 (tt0) cc_final: 0.7591 (tt0) REVERT: G 114 VAL cc_start: 0.8286 (m) cc_final: 0.8065 (p) REVERT: H 32 GLU cc_start: 0.7034 (pp20) cc_final: 0.6193 (pp20) REVERT: K 148 MET cc_start: 0.3884 (mtp) cc_final: 0.3527 (mtt) REVERT: K 354 SER cc_start: 0.5909 (m) cc_final: 0.5314 (p) REVERT: K 429 MET cc_start: 0.5935 (mtp) cc_final: 0.5671 (mtp) REVERT: K 605 MET cc_start: 0.8258 (tpp) cc_final: 0.7892 (tpp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3247 time to fit residues: 55.3903 Evaluate side-chains 99 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [33, 40, 123, 106, 80, 157, 117, 24, 45, 137, 75] chunk 33 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 80 optimal weight: 50.0000 chunk 157 optimal weight: 30.0000 chunk 117 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 75 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.113188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.087746 restraints weight = 197333.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.088216 restraints weight = 174701.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.088830 restraints weight = 110130.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.089086 restraints weight = 88356.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.089115 restraints weight = 83876.548| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17733 Z= 0.311 Angle : 0.733 14.849 25165 Z= 0.433 Chirality : 0.044 0.175 2794 Planarity : 0.006 0.060 2229 Dihedral : 28.058 89.680 4696 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.22), residues: 1342 helix: 1.03 (0.19), residues: 681 sheet: -1.49 (0.63), residues: 66 loop : -1.05 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 92 TYR 0.026 0.002 TYR K 547 PHE 0.035 0.003 PHE A 104 TRP 0.033 0.003 TRP K 694 HIS 0.010 0.002 HIS K 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.31 (17714) covalent geometry : angle 0.71460 / 0.43 (25147) hydrogen bonds : bond 0.06592 / 4.55 ( 909) hydrogen bonds : angle 4.39866 / 3.12 ( 2309) metal coordination : bond 0.00821 / 0.56 ( 19) metal coordination : angle 6.12907 / 3.84 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 MET cc_start: 0.7589 (tpp) cc_final: 0.7216 (tpp) REVERT: G 35 ARG cc_start: 0.8282 (mtm110) cc_final: 0.8056 (ttp-110) REVERT: G 114 VAL cc_start: 0.8400 (m) cc_final: 0.8176 (p) REVERT: K 148 MET cc_start: 0.3890 (mtp) cc_final: 0.3537 (mtt) REVERT: K 354 SER cc_start: 0.5941 (m) cc_final: 0.5352 (p) REVERT: K 429 MET cc_start: 0.6202 (mtp) cc_final: 0.5939 (mtp) REVERT: K 605 MET cc_start: 0.8384 (tpp) cc_final: 0.8039 (tpp) outliers start: 1 outliers final: 1 residues processed: 110 average time/residue: 0.3288 time to fit residues: 51.5650 Evaluate side-chains 92 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [29, 44, 103, 126, 95, 137, 136, 75, 53, 56, 146] chunk 29 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 103 optimal weight: 50.0000 chunk 126 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 137 optimal weight: 20.0000 chunk 136 optimal weight: 0.8980 chunk 75 optimal weight: 50.0000 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 146 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 GLN K 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.115868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.090375 restraints weight = 197539.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.090482 restraints weight = 158674.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.091718 restraints weight = 102619.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.091599 restraints weight = 79563.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.091763 restraints weight = 76930.580| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17733 Z= 0.137 Angle : 0.602 12.839 25165 Z= 0.371 Chirality : 0.040 0.154 2794 Planarity : 0.006 0.150 2229 Dihedral : 27.982 86.895 4696 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.23), residues: 1342 helix: 1.62 (0.20), residues: 680 sheet: -1.53 (0.62), residues: 71 loop : -0.83 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.016 0.002 TYR D 80 PHE 0.024 0.002 PHE K 722 TRP 0.028 0.002 TRP K 694 HIS 0.006 0.001 HIS K 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.14 (17714) covalent geometry : angle 0.58412 / 0.37 (25147) hydrogen bonds : bond 0.04945 / 3.34 ( 909) hydrogen bonds : angle 3.74422 / 2.65 ( 2309) metal coordination : bond 0.00504 / 0.33 ( 19) metal coordination : angle 5.53608 / 3.46 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4545.45 seconds wall clock time: 78 minutes 9.59 seconds (4689.59 seconds total)