Starting phenix.real_space_refine on Sun Mar 17 16:45:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/03_2024/6r1u_4705_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/03_2024/6r1u_4705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/03_2024/6r1u_4705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/03_2024/6r1u_4705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/03_2024/6r1u_4705_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/03_2024/6r1u_4705_updated.pdb" } resolution = 4.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 296 5.49 5 S 54 5.16 5 C 10684 2.51 5 N 3372 2.21 5 O 3985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 129": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "K GLU 54": "OE1" <-> "OE2" Residue "K ARG 72": "NH1" <-> "NH2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K GLU 146": "OE1" <-> "OE2" Residue "K ARG 148": "NH1" <-> "NH2" Residue "K ARG 151": "NH1" <-> "NH2" Residue "K GLU 156": "OE1" <-> "OE2" Residue "K GLU 189": "OE1" <-> "OE2" Residue "K GLU 195": "OE1" <-> "OE2" Residue "K GLU 290": "OE1" <-> "OE2" Residue "K GLU 296": "OE1" <-> "OE2" Residue "K GLU 324": "OE1" <-> "OE2" Residue "K ARG 338": "NH1" <-> "NH2" Residue "K GLU 348": "OE1" <-> "OE2" Residue "K GLU 452": "OE1" <-> "OE2" Residue "K ARG 464": "NH1" <-> "NH2" Residue "K GLU 470": "OE1" <-> "OE2" Residue "K GLU 496": "OE1" <-> "OE2" Residue "K ARG 498": "NH1" <-> "NH2" Residue "K GLU 511": "OE1" <-> "OE2" Residue "K GLU 515": "OE1" <-> "OE2" Residue "K GLU 523": "OE1" <-> "OE2" Residue "K GLU 530": "OE1" <-> "OE2" Residue "K GLU 532": "OE1" <-> "OE2" Residue "K GLU 563": "OE1" <-> "OE2" Residue "K GLU 584": "OE1" <-> "OE2" Residue "K GLU 588": "OE1" <-> "OE2" Residue "K GLU 645": "OE1" <-> "OE2" Residue "K GLU 660": "OE1" <-> "OE2" Residue "K GLU 716": "OE1" <-> "OE2" Residue "K GLU 743": "OE1" <-> "OE2" Residue "K GLU 795": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18394 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 689 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 811 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 820 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 870 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "H" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 775 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 5837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5837 Classifications: {'peptide': 737} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 36, 'TRANS': 698} Chain breaks: 2 Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "M" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 193 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "K" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' ZN': 3, 'FAD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12239 SG CYS K 53 75.441 111.267 70.128 1.00 48.02 S ATOM 12272 SG CYS K 58 73.966 113.629 73.201 1.00 47.27 S ATOM 12317 SG CYS K 65 85.145 104.914 75.500 1.00 37.13 S ATOM 12376 SG CYS K 73 88.895 105.346 75.202 1.00 40.55 S ATOM 12534 SG CYS K 92 86.794 104.861 71.584 1.00 37.37 S ATOM 12557 SG CYS K 95 87.344 102.062 74.063 1.00 36.80 S ATOM 12964 SG CYS K 142 77.571 111.293 100.726 1.00 35.45 S ATOM 13002 SG CYS K 147 77.414 114.859 99.519 1.00 37.39 S ATOM 13195 SG CYS K 169 80.000 112.370 98.082 1.00 34.97 S ATOM 13246 SG CYS K 185 80.326 113.849 101.839 1.00 38.56 S Time building chain proxies: 9.90, per 1000 atoms: 0.54 Number of scatterers: 18394 At special positions: 0 Unit cell: (134.62, 132.5, 137.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 54 16.00 P 296 15.00 O 3985 8.00 N 3372 7.00 C 10684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 9765 O5' DC J -46 .*. O " rejected from bonding due to valence issues. Atom "ATOM 9765 O5' DC J -46 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.72 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 902 " pdb="ZN ZN K 902 " - pdb=" NE2 HIS K 90 " pdb="ZN ZN K 902 " - pdb=" SG CYS K 58 " pdb="ZN ZN K 902 " - pdb=" ND1 HIS K 84 " pdb="ZN ZN K 902 " - pdb=" SG CYS K 53 " pdb=" ZN K 903 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 95 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 65 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 73 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 92 " pdb=" ZN K 904 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 147 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 142 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 185 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 169 " Number of angles added : 13 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 7 sheets defined 48.4% alpha, 4.6% beta 142 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 9.67 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 78 removed outlier: 4.087A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.677A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 47 through 73 removed outlier: 4.332A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 78 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 119 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 86 through 114 Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 74 Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 18 through 21 No H-bonds generated for 'chain 'G' and resid 18 through 21' Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 47 through 72 Processing helix chain 'G' and resid 80 through 87 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 102 through 119 removed outlier: 3.603A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 100 Processing helix chain 'K' and resid 107 through 116 Processing helix chain 'K' and resid 127 through 134 Processing helix chain 'K' and resid 161 through 166 Processing helix chain 'K' and resid 184 through 186 No H-bonds generated for 'chain 'K' and resid 184 through 186' Processing helix chain 'K' and resid 192 through 197 removed outlier: 3.673A pdb=" N VAL K 196 " --> pdb=" O ARG K 192 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER K 197 " --> pdb=" O VAL K 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 192 through 197' Processing helix chain 'K' and resid 199 through 204 removed outlier: 3.984A pdb=" N SER K 203 " --> pdb=" O HIS K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 219 No H-bonds generated for 'chain 'K' and resid 217 through 219' Processing helix chain 'K' and resid 225 through 227 No H-bonds generated for 'chain 'K' and resid 225 through 227' Processing helix chain 'K' and resid 291 through 296 Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 305 through 320 Processing helix chain 'K' and resid 328 through 334 Proline residue: K 333 - end of helix Processing helix chain 'K' and resid 340 through 359 removed outlier: 3.628A pdb=" N VAL K 349 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU K 350 " --> pdb=" O GLN K 347 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS K 359 " --> pdb=" O MET K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 378 through 380 No H-bonds generated for 'chain 'K' and resid 378 through 380' Processing helix chain 'K' and resid 392 through 404 Processing helix chain 'K' and resid 446 through 454 Processing helix chain 'K' and resid 477 through 500 removed outlier: 3.963A pdb=" N LYS K 499 " --> pdb=" O SER K 495 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP K 500 " --> pdb=" O GLU K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 503 through 505 No H-bonds generated for 'chain 'K' and resid 503 through 505' Processing helix chain 'K' and resid 509 through 523 Processing helix chain 'K' and resid 530 through 547 Processing helix chain 'K' and resid 561 through 564 Processing helix chain 'K' and resid 579 through 587 removed outlier: 3.615A pdb=" N GLU K 584 " --> pdb=" O VAL K 581 " (cutoff:3.500A) Processing helix chain 'K' and resid 629 through 634 Processing helix chain 'K' and resid 645 through 653 Processing helix chain 'K' and resid 672 through 675 No H-bonds generated for 'chain 'K' and resid 672 through 675' Processing helix chain 'K' and resid 688 through 690 No H-bonds generated for 'chain 'K' and resid 688 through 690' Processing helix chain 'K' and resid 715 through 721 Processing helix chain 'K' and resid 726 through 740 Processing helix chain 'K' and resid 757 through 759 No H-bonds generated for 'chain 'K' and resid 757 through 759' Processing helix chain 'K' and resid 776 through 783 removed outlier: 3.544A pdb=" N ILE K 782 " --> pdb=" O TYR K 779 " (cutoff:3.500A) Processing helix chain 'K' and resid 795 through 797 No H-bonds generated for 'chain 'K' and resid 795 through 797' Processing helix chain 'K' and resid 805 through 821 Processing helix chain 'L' and resid 220 through 222 No H-bonds generated for 'chain 'L' and resid 220 through 222' Processing helix chain 'M' and resid 2 through 4 No H-bonds generated for 'chain 'M' and resid 2 through 4' Processing sheet with id= A, first strand: chain 'K' and resid 139 through 141 Processing sheet with id= B, first strand: chain 'K' and resid 407 through 411 removed outlier: 6.869A pdb=" N LYS K 622 " --> pdb=" O ILE K 386 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE K 388 " --> pdb=" O LYS K 622 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU K 624 " --> pdb=" O ILE K 388 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 438 through 440 Processing sheet with id= D, first strand: chain 'K' and resid 467 through 469 removed outlier: 8.552A pdb=" N ILE K 468 " --> pdb=" O PHE K 680 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY K 682 " --> pdb=" O ILE K 468 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL K 696 " --> pdb=" O VAL K 712 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL K 712 " --> pdb=" O VAL K 696 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS K 751 " --> pdb=" O GLN K 665 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'K' and resid 638 through 640 removed outlier: 6.756A pdb=" N THR K 611 " --> pdb=" O GLN K 599 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE K 601 " --> pdb=" O GLN K 609 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLN K 609 " --> pdb=" O ILE K 601 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 654 through 657 Processing sheet with id= G, first strand: chain 'K' and resid 82 through 86 removed outlier: 6.486A pdb=" N GLU K 89 " --> pdb=" O LEU K 85 " (cutoff:3.500A) 517 hydrogen bonds defined for protein. 1455 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 9.79 Time building geometry restraints manager: 10.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2389 1.31 - 1.44: 6635 1.44 - 1.57: 9668 1.57 - 1.70: 586 1.70 - 1.82: 81 Bond restraints: 19359 Sorted by residual: bond pdb=" O5B FAD K 901 " pdb=" PA FAD K 901 " ideal model delta sigma weight residual 1.634 1.386 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" O3P FAD K 901 " pdb=" P FAD K 901 " ideal model delta sigma weight residual 1.660 1.470 0.190 2.00e-02 2.50e+03 9.07e+01 bond pdb=" O3P FAD K 901 " pdb=" PA FAD K 901 " ideal model delta sigma weight residual 1.633 1.454 0.179 2.00e-02 2.50e+03 8.05e+01 bond pdb=" O5' FAD K 901 " pdb=" P FAD K 901 " ideal model delta sigma weight residual 1.637 1.464 0.173 2.00e-02 2.50e+03 7.48e+01 bond pdb=" O1A FAD K 901 " pdb=" PA FAD K 901 " ideal model delta sigma weight residual 1.509 1.365 0.144 2.00e-02 2.50e+03 5.22e+01 ... (remaining 19354 not shown) Histogram of bond angle deviations from ideal: 95.39 - 103.14: 708 103.14 - 110.90: 8207 110.90 - 118.66: 7874 118.66 - 126.41: 9670 126.41 - 134.17: 964 Bond angle restraints: 27423 Sorted by residual: angle pdb=" C LYS K 75 " pdb=" CA LYS K 75 " pdb=" CB LYS K 75 " ideal model delta sigma weight residual 117.23 108.32 8.91 1.36e+00 5.41e-01 4.29e+01 angle pdb=" O1P FAD K 901 " pdb=" P FAD K 901 " pdb=" O2P FAD K 901 " ideal model delta sigma weight residual 122.50 105.35 17.15 3.00e+00 1.11e-01 3.27e+01 angle pdb=" C ASP L 214 " pdb=" N PRO L 215 " pdb=" CA PRO L 215 " ideal model delta sigma weight residual 119.47 125.97 -6.50 1.16e+00 7.43e-01 3.14e+01 angle pdb=" CA LYS K 75 " pdb=" C LYS K 75 " pdb=" N ASN K 76 " ideal model delta sigma weight residual 119.98 115.33 4.65 8.50e-01 1.38e+00 3.00e+01 angle pdb=" C ASP K 760 " pdb=" N PRO K 761 " pdb=" CA PRO K 761 " ideal model delta sigma weight residual 119.05 125.04 -5.99 1.11e+00 8.12e-01 2.92e+01 ... (remaining 27418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 9220 35.91 - 71.82: 1648 71.82 - 107.73: 32 107.73 - 143.64: 1 143.64 - 179.56: 1 Dihedral angle restraints: 10902 sinusoidal: 6408 harmonic: 4494 Sorted by residual: dihedral pdb=" CD ARG A 40 " pdb=" NE ARG A 40 " pdb=" CZ ARG A 40 " pdb=" NH1 ARG A 40 " ideal model delta sinusoidal sigma weight residual 0.00 -85.61 85.61 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CD ARG G 11 " pdb=" NE ARG G 11 " pdb=" CZ ARG G 11 " pdb=" NH1 ARG G 11 " ideal model delta sinusoidal sigma weight residual 0.00 -66.88 66.88 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CD ARG H 30 " pdb=" NE ARG H 30 " pdb=" CZ ARG H 30 " pdb=" NH1 ARG H 30 " ideal model delta sinusoidal sigma weight residual 0.00 -57.45 57.45 1 1.00e+01 1.00e-02 4.43e+01 ... (remaining 10899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2312 0.062 - 0.124: 630 0.124 - 0.186: 107 0.186 - 0.247: 16 0.247 - 0.309: 3 Chirality restraints: 3068 Sorted by residual: chirality pdb=" C3' FAD K 901 " pdb=" C2' FAD K 901 " pdb=" C4' FAD K 901 " pdb=" O3' FAD K 901 " both_signs ideal model delta sigma weight residual False -2.55 -2.24 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA THR K 143 " pdb=" N THR K 143 " pdb=" C THR K 143 " pdb=" CB THR K 143 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU G 34 " pdb=" CB LEU G 34 " pdb=" CD1 LEU G 34 " pdb=" CD2 LEU G 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3065 not shown) Planarity restraints: 2456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FAD K 901 " -0.396 2.00e-02 2.50e+03 2.24e-01 2.38e+03 pdb=" C10 FAD K 901 " -0.140 2.00e-02 2.50e+03 pdb=" C2 FAD K 901 " 0.214 2.00e-02 2.50e+03 pdb=" C4 FAD K 901 " 0.037 2.00e-02 2.50e+03 pdb=" C4X FAD K 901 " -0.149 2.00e-02 2.50e+03 pdb=" C5X FAD K 901 " -0.219 2.00e-02 2.50e+03 pdb=" C6 FAD K 901 " -0.124 2.00e-02 2.50e+03 pdb=" C7 FAD K 901 " 0.076 2.00e-02 2.50e+03 pdb=" C7M FAD K 901 " 0.199 2.00e-02 2.50e+03 pdb=" C8 FAD K 901 " 0.173 2.00e-02 2.50e+03 pdb=" C8M FAD K 901 " 0.382 2.00e-02 2.50e+03 pdb=" C9 FAD K 901 " 0.055 2.00e-02 2.50e+03 pdb=" C9A FAD K 901 " -0.148 2.00e-02 2.50e+03 pdb=" N1 FAD K 901 " 0.045 2.00e-02 2.50e+03 pdb=" N10 FAD K 901 " -0.262 2.00e-02 2.50e+03 pdb=" N3 FAD K 901 " 0.222 2.00e-02 2.50e+03 pdb=" N5 FAD K 901 " -0.369 2.00e-02 2.50e+03 pdb=" O2 FAD K 901 " 0.371 2.00e-02 2.50e+03 pdb=" O4 FAD K 901 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 40 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 40 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 40 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 40 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 40 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 11 " 1.007 9.50e-02 1.11e+02 4.51e-01 1.23e+02 pdb=" NE ARG G 11 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG G 11 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG G 11 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 11 " 0.023 2.00e-02 2.50e+03 ... (remaining 2453 not shown) Histogram of nonbonded interaction distances: 0.54 - 1.42: 11 1.42 - 2.29: 64 2.29 - 3.16: 14617 3.16 - 4.03: 54964 4.03 - 4.90: 89350 Warning: very small nonbonded interaction distances. Nonbonded interactions: 159006 Sorted by model distance: nonbonded pdb=" NH1 ARG H 30 " pdb=" O5' DC J -46 " model vdw 0.544 2.520 nonbonded pdb=" NH2 ARG H 30 " pdb=" O3' DT J -47 " model vdw 0.796 2.520 nonbonded pdb=" CB ARG A 128 " pdb=" OE1 GLU A 133 " model vdw 0.821 3.440 nonbonded pdb=" NE ARG A 128 " pdb=" OE2 GLU A 133 " model vdw 0.827 2.520 nonbonded pdb=" NZ LYS D 28 " pdb=" O3' DA J 50 " model vdw 0.922 2.520 ... (remaining 159001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 134) selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 101) selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 120) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 26 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.440 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 63.600 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4616 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 0.248 19359 Z= 0.521 Angle : 1.043 17.149 27423 Z= 0.634 Chirality : 0.058 0.309 3068 Planarity : 0.023 0.492 2456 Dihedral : 25.719 179.556 8006 Min Nonbonded Distance : 0.544 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 1.25 % Allowed : 4.66 % Favored : 94.09 % Rotamer: Outliers : 6.26 % Allowed : 4.58 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.18), residues: 1524 helix: -2.27 (0.14), residues: 787 sheet: 0.51 (0.69), residues: 61 loop : -1.71 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 117 HIS 0.014 0.002 HIS B 75 PHE 0.033 0.003 PHE C 25 TYR 0.019 0.003 TYR K 767 ARG 0.016 0.001 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 276 time to evaluate : 1.698 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: A 48 LEU cc_start: 0.8726 (mp) cc_final: 0.8345 (tp) REVERT: E 74 ILE cc_start: 0.9194 (mt) cc_final: 0.8614 (mm) REVERT: E 107 THR cc_start: 0.8394 (m) cc_final: 0.8033 (p) REVERT: F 88 TYR cc_start: 0.8176 (m-10) cc_final: 0.7941 (m-80) REVERT: K 85 LEU cc_start: 0.1545 (OUTLIER) cc_final: 0.1162 (tp) REVERT: K 204 MET cc_start: 0.2224 (mtm) cc_final: 0.1943 (ttm) REVERT: K 294 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6212 (mt) REVERT: K 458 MET cc_start: -0.1180 (mtm) cc_final: -0.3741 (mtt) REVERT: K 700 MET cc_start: -0.2175 (mmm) cc_final: -0.2801 (mmm) REVERT: M 22 THR cc_start: -0.0210 (OUTLIER) cc_final: -0.0427 (t) outliers start: 82 outliers final: 26 residues processed: 347 average time/residue: 0.4129 time to fit residues: 196.0624 Evaluate side-chains 150 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 50.0000 chunk 134 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 138 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 40.0000 chunk 160 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 81 ASN D 92 GLN E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 110 ASN H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN K 276 ASN K 400 GLN K 469 GLN ** K 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 218 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4886 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 19359 Z= 0.339 Angle : 0.718 7.389 27423 Z= 0.409 Chirality : 0.042 0.189 3068 Planarity : 0.007 0.135 2456 Dihedral : 29.557 177.578 4968 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.54 % Favored : 96.26 % Rotamer: Outliers : 0.23 % Allowed : 2.98 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.20), residues: 1524 helix: 0.09 (0.17), residues: 802 sheet: 1.17 (0.65), residues: 61 loop : -0.81 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 762 HIS 0.010 0.001 HIS F 75 PHE 0.019 0.002 PHE E 104 TYR 0.023 0.002 TYR B 88 ARG 0.020 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 1.711 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: B 84 MET cc_start: 0.8044 (mmm) cc_final: 0.6239 (tpp) REVERT: E 74 ILE cc_start: 0.9011 (mt) cc_final: 0.8739 (tt) REVERT: E 100 LEU cc_start: 0.8701 (mm) cc_final: 0.8500 (mm) REVERT: F 59 LYS cc_start: 0.8998 (tptp) cc_final: 0.8546 (tppt) REVERT: H 73 GLU cc_start: 0.8182 (tp30) cc_final: 0.7964 (tp30) REVERT: K 265 MET cc_start: -0.2665 (ttt) cc_final: -0.3088 (tpt) REVERT: K 458 MET cc_start: -0.1494 (mtm) cc_final: -0.3583 (mtt) outliers start: 3 outliers final: 0 residues processed: 168 average time/residue: 0.3805 time to fit residues: 93.2876 Evaluate side-chains 110 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 161 optimal weight: 0.0670 chunk 173 optimal weight: 9.9990 chunk 143 optimal weight: 50.0000 chunk 159 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 129 optimal weight: 40.0000 overall best weight: 3.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 89 ASN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS K 98 HIS ** K 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4931 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19359 Z= 0.236 Angle : 0.627 6.519 27423 Z= 0.358 Chirality : 0.039 0.158 3068 Planarity : 0.005 0.074 2456 Dihedral : 29.625 177.958 4968 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.22 % Favored : 96.52 % Rotamer: Outliers : 0.23 % Allowed : 3.59 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1524 helix: 0.81 (0.18), residues: 804 sheet: 1.38 (0.60), residues: 71 loop : -0.51 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 762 HIS 0.012 0.001 HIS E 39 PHE 0.015 0.001 PHE A 104 TYR 0.021 0.002 TYR K 99 ARG 0.007 0.001 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 154 time to evaluate : 1.719 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: B 84 MET cc_start: 0.8114 (mmm) cc_final: 0.7464 (tpp) REVERT: E 74 ILE cc_start: 0.9030 (mt) cc_final: 0.8760 (tt) REVERT: F 59 LYS cc_start: 0.8917 (tptp) cc_final: 0.8654 (tppt) REVERT: G 104 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7685 (tp-100) REVERT: H 73 GLU cc_start: 0.8069 (tp30) cc_final: 0.7733 (tp30) REVERT: H 76 ARG cc_start: 0.8459 (ptp90) cc_final: 0.8236 (ptp90) REVERT: K 204 MET cc_start: 0.2142 (mtm) cc_final: 0.1718 (ttm) REVERT: K 265 MET cc_start: -0.2687 (ttt) cc_final: -0.3026 (tpt) REVERT: K 458 MET cc_start: -0.1899 (mtm) cc_final: -0.3715 (mtt) REVERT: K 700 MET cc_start: -0.2618 (mmt) cc_final: -0.3007 (mmp) outliers start: 3 outliers final: 0 residues processed: 157 average time/residue: 0.3622 time to fit residues: 82.8896 Evaluate side-chains 104 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 1.9990 chunk 121 optimal weight: 30.0000 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 108 optimal weight: 50.0000 chunk 161 optimal weight: 30.0000 chunk 171 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5098 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19359 Z= 0.346 Angle : 0.656 7.386 27423 Z= 0.373 Chirality : 0.040 0.172 3068 Planarity : 0.005 0.067 2456 Dihedral : 29.662 177.572 4968 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.08 % Favored : 96.72 % Rotamer: Outliers : 0.08 % Allowed : 3.13 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1524 helix: 0.95 (0.18), residues: 813 sheet: 1.60 (0.60), residues: 71 loop : -0.36 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 762 HIS 0.013 0.001 HIS F 75 PHE 0.026 0.001 PHE E 104 TYR 0.036 0.002 TYR B 88 ARG 0.012 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.689 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: B 84 MET cc_start: 0.8326 (mmm) cc_final: 0.8019 (mmm) REVERT: B 88 TYR cc_start: 0.8671 (m-80) cc_final: 0.8430 (m-80) REVERT: H 73 GLU cc_start: 0.8242 (tp30) cc_final: 0.7707 (tp30) REVERT: H 76 ARG cc_start: 0.8454 (ptp90) cc_final: 0.8171 (ptp90) REVERT: K 204 MET cc_start: 0.2336 (mtm) cc_final: 0.1564 (ttm) REVERT: K 458 MET cc_start: -0.2036 (mtm) cc_final: -0.3814 (mtt) outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.3321 time to fit residues: 63.3650 Evaluate side-chains 89 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5082 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19359 Z= 0.269 Angle : 0.613 7.583 27423 Z= 0.349 Chirality : 0.039 0.152 3068 Planarity : 0.004 0.060 2456 Dihedral : 29.767 177.541 4968 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.08 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1524 helix: 1.26 (0.18), residues: 806 sheet: 1.62 (0.61), residues: 72 loop : -0.34 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.010 0.001 HIS D 106 PHE 0.013 0.001 PHE K 753 TYR 0.024 0.001 TYR B 88 ARG 0.010 0.001 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.625 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: B 84 MET cc_start: 0.8155 (mmm) cc_final: 0.7909 (mmm) REVERT: E 106 ASP cc_start: 0.7576 (m-30) cc_final: 0.6986 (m-30) REVERT: F 49 LEU cc_start: 0.9025 (mp) cc_final: 0.8744 (mp) REVERT: H 73 GLU cc_start: 0.8334 (tp30) cc_final: 0.7766 (tp30) REVERT: H 76 ARG cc_start: 0.8433 (ptp90) cc_final: 0.8183 (ptp90) REVERT: K 204 MET cc_start: 0.2064 (mtm) cc_final: 0.1475 (ttm) REVERT: K 458 MET cc_start: -0.2229 (mtm) cc_final: -0.3969 (mtt) REVERT: K 700 MET cc_start: -0.2828 (mmt) cc_final: -0.3112 (mmt) REVERT: M 4 MET cc_start: -0.0990 (ppp) cc_final: -0.2527 (ptm) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3351 time to fit residues: 62.7051 Evaluate side-chains 92 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 171 optimal weight: 30.0000 chunk 142 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5053 moved from start: 0.6325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19359 Z= 0.210 Angle : 0.580 8.889 27423 Z= 0.330 Chirality : 0.038 0.157 3068 Planarity : 0.004 0.057 2456 Dihedral : 29.632 178.225 4968 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.95 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.22), residues: 1524 helix: 1.41 (0.18), residues: 807 sheet: 1.67 (0.61), residues: 72 loop : -0.26 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.008 0.001 HIS D 106 PHE 0.013 0.001 PHE K 753 TYR 0.026 0.001 TYR B 88 ARG 0.008 0.000 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.600 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: A 97 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8375 (mt-10) REVERT: C 114 VAL cc_start: 0.9006 (t) cc_final: 0.8773 (t) REVERT: E 105 GLU cc_start: 0.6769 (pp20) cc_final: 0.6473 (pp20) REVERT: E 106 ASP cc_start: 0.7227 (m-30) cc_final: 0.6899 (m-30) REVERT: H 73 GLU cc_start: 0.8258 (tp30) cc_final: 0.7970 (tp30) REVERT: K 204 MET cc_start: 0.2151 (mtm) cc_final: 0.1668 (ttt) REVERT: K 458 MET cc_start: -0.2304 (mtm) cc_final: -0.4019 (mtt) REVERT: K 700 MET cc_start: -0.2599 (mmt) cc_final: -0.3096 (mmm) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.3201 time to fit residues: 61.1306 Evaluate side-chains 89 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 40.0000 chunk 19 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 125 optimal weight: 0.0000 chunk 96 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 170 optimal weight: 50.0000 chunk 106 optimal weight: 30.0000 chunk 104 optimal weight: 50.0000 chunk 78 optimal weight: 6.9990 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5223 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 19359 Z= 0.415 Angle : 0.683 8.011 27423 Z= 0.388 Chirality : 0.042 0.187 3068 Planarity : 0.005 0.060 2456 Dihedral : 29.926 176.915 4968 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1524 helix: 1.06 (0.18), residues: 805 sheet: 1.69 (0.61), residues: 72 loop : -0.31 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 762 HIS 0.012 0.001 HIS F 75 PHE 0.012 0.001 PHE K 753 TYR 0.037 0.002 TYR E 54 ARG 0.010 0.001 ARG G 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8331 (mt-10) REVERT: E 105 GLU cc_start: 0.7241 (pp20) cc_final: 0.6945 (pp20) REVERT: K 131 MET cc_start: 0.4193 (mpp) cc_final: 0.3819 (mpp) REVERT: K 204 MET cc_start: 0.2223 (mtm) cc_final: 0.1746 (ttt) REVERT: K 265 MET cc_start: -0.1463 (tpt) cc_final: -0.1949 (tpt) REVERT: K 306 MET cc_start: 0.1238 (tmm) cc_final: 0.0524 (tpt) REVERT: K 458 MET cc_start: -0.2372 (mtm) cc_final: -0.4080 (mtt) REVERT: K 700 MET cc_start: -0.2142 (mmt) cc_final: -0.2606 (mmm) REVERT: K 710 MET cc_start: -0.1710 (tmm) cc_final: -0.2056 (tmm) REVERT: M 4 MET cc_start: -0.0923 (ppp) cc_final: -0.1780 (ptm) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3269 time to fit residues: 50.7374 Evaluate side-chains 73 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 30.0000 chunk 68 optimal weight: 4.9990 chunk 101 optimal weight: 0.0570 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 108 optimal weight: 0.0470 chunk 116 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 134 optimal weight: 50.0000 chunk 155 optimal weight: 5.9990 overall best weight: 2.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 HIS ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5091 moved from start: 0.7235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19359 Z= 0.201 Angle : 0.604 9.462 27423 Z= 0.341 Chirality : 0.038 0.186 3068 Planarity : 0.004 0.053 2456 Dihedral : 29.807 178.747 4968 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.82 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1524 helix: 1.36 (0.18), residues: 794 sheet: 1.65 (0.62), residues: 72 loop : -0.27 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.007 0.001 HIS F 75 PHE 0.013 0.001 PHE K 753 TYR 0.037 0.001 TYR B 88 ARG 0.005 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8220 (mt-10) REVERT: B 84 MET cc_start: 0.8410 (mmm) cc_final: 0.8093 (tpp) REVERT: H 73 GLU cc_start: 0.8121 (tp30) cc_final: 0.7167 (tp30) REVERT: K 204 MET cc_start: 0.2141 (mtm) cc_final: 0.1834 (ttt) REVERT: K 265 MET cc_start: -0.1236 (tpt) cc_final: -0.1681 (tpt) REVERT: K 306 MET cc_start: 0.1378 (tmm) cc_final: 0.0605 (tpt) REVERT: K 458 MET cc_start: -0.2329 (mtm) cc_final: -0.4096 (mtt) REVERT: K 700 MET cc_start: -0.2135 (mmt) cc_final: -0.2620 (mmm) REVERT: K 710 MET cc_start: -0.1545 (tmm) cc_final: -0.1904 (tmm) REVERT: M 4 MET cc_start: -0.1221 (ppp) cc_final: -0.2101 (ptm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3439 time to fit residues: 55.9216 Evaluate side-chains 77 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 10.0000 chunk 149 optimal weight: 40.0000 chunk 158 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 124 optimal weight: 50.0000 chunk 48 optimal weight: 0.6980 chunk 143 optimal weight: 40.0000 chunk 150 optimal weight: 20.0000 chunk 104 optimal weight: 40.0000 chunk 168 optimal weight: 50.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 539 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5220 moved from start: 0.7747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 19359 Z= 0.386 Angle : 0.661 8.961 27423 Z= 0.373 Chirality : 0.040 0.158 3068 Planarity : 0.005 0.057 2456 Dihedral : 29.901 177.693 4968 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.54 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.21), residues: 1524 helix: 1.08 (0.18), residues: 801 sheet: 1.64 (0.61), residues: 72 loop : -0.27 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.010 0.001 HIS F 75 PHE 0.019 0.001 PHE K 753 TYR 0.032 0.001 TYR E 54 ARG 0.006 0.001 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8244 (mt-10) REVERT: F 49 LEU cc_start: 0.9323 (mp) cc_final: 0.8889 (mp) REVERT: F 59 LYS cc_start: 0.9046 (mmmm) cc_final: 0.8732 (mmmm) REVERT: H 73 GLU cc_start: 0.8307 (tp30) cc_final: 0.7667 (tp30) REVERT: K 131 MET cc_start: 0.4159 (mpp) cc_final: 0.3737 (mpp) REVERT: K 204 MET cc_start: 0.2187 (mtm) cc_final: 0.1829 (ttt) REVERT: K 265 MET cc_start: -0.1182 (tpt) cc_final: -0.1621 (tpt) REVERT: K 306 MET cc_start: 0.1196 (tmm) cc_final: 0.0611 (tpt) REVERT: K 458 MET cc_start: -0.2110 (mtm) cc_final: -0.3995 (mtt) REVERT: K 700 MET cc_start: -0.1946 (mmt) cc_final: -0.2438 (mmm) REVERT: K 710 MET cc_start: -0.1206 (tmm) cc_final: -0.1649 (tmm) REVERT: M 4 MET cc_start: -0.1108 (ppp) cc_final: -0.2011 (ptm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3390 time to fit residues: 50.6257 Evaluate side-chains 71 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 50.0000 chunk 79 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 176 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 108 optimal weight: 30.0000 chunk 86 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 149 optimal weight: 50.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5182 moved from start: 0.7897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19359 Z= 0.300 Angle : 0.623 9.395 27423 Z= 0.353 Chirality : 0.039 0.159 3068 Planarity : 0.004 0.053 2456 Dihedral : 29.895 178.246 4968 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.02 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.21), residues: 1524 helix: 1.10 (0.18), residues: 801 sheet: 1.62 (0.61), residues: 72 loop : -0.23 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.009 0.001 HIS F 75 PHE 0.014 0.001 PHE K 753 TYR 0.026 0.001 TYR E 54 ARG 0.005 0.001 ARG F 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8215 (mt-10) REVERT: F 49 LEU cc_start: 0.9345 (mp) cc_final: 0.8924 (mp) REVERT: F 59 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8741 (mmmm) REVERT: H 73 GLU cc_start: 0.8280 (tp30) cc_final: 0.7470 (tp30) REVERT: K 131 MET cc_start: 0.4223 (mpp) cc_final: 0.3847 (mpp) REVERT: K 204 MET cc_start: 0.2167 (mtm) cc_final: 0.1822 (ttt) REVERT: K 265 MET cc_start: -0.1171 (tpt) cc_final: -0.1577 (tpt) REVERT: K 306 MET cc_start: 0.1079 (tmm) cc_final: 0.0495 (tpt) REVERT: K 458 MET cc_start: -0.2235 (mtm) cc_final: -0.4620 (mtt) REVERT: K 700 MET cc_start: -0.2074 (mmt) cc_final: -0.2514 (mmm) REVERT: K 710 MET cc_start: -0.1291 (tmm) cc_final: -0.1741 (tmm) REVERT: M 4 MET cc_start: -0.1030 (ppp) cc_final: -0.1917 (ptm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3279 time to fit residues: 49.5617 Evaluate side-chains 75 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 20 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.099670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.052651 restraints weight = 196460.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.046622 restraints weight = 117171.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.045551 restraints weight = 82477.717| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.7847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19359 Z= 0.171 Angle : 0.599 10.567 27423 Z= 0.332 Chirality : 0.038 0.163 3068 Planarity : 0.004 0.053 2456 Dihedral : 29.529 179.339 4968 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.22), residues: 1524 helix: 1.41 (0.19), residues: 791 sheet: 1.50 (0.60), residues: 72 loop : -0.17 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.005 0.001 HIS B 75 PHE 0.014 0.001 PHE K 753 TYR 0.015 0.001 TYR A 54 ARG 0.008 0.000 ARG B 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3659.35 seconds wall clock time: 67 minutes 34.29 seconds (4054.29 seconds total)