Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 18:46:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/04_2023/6r1u_4705_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/04_2023/6r1u_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_4705/04_2023/6r1u_4705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/04_2023/6r1u_4705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/04_2023/6r1u_4705_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/04_2023/6r1u_4705_updated.pdb" } resolution = 4.36 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 9.34, per 1000 atoms: 0.51 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: 9.48 Conformation dependent library (CDL) restraints added in 1.7 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: 8.06 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: 10.38 Time building geometry restraints manager: 9.90 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: 8967 35.91 - 71.82: 1598 71.82 - 107.73: 32 107.73 - 143.64: 1 143.64 - 179.56: 1 Dihedral angle restraints: 10599 sinusoidal: 6105 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 10596 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.500 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 61.540 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.460 ------------------------------------------------------------------------------- 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 : 25.650 179.556 7703 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 % 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 *********************** 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 : 1.815 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 outliers start: 82 outliers final: 26 residues processed: 347 average time/residue: 0.4257 time to fit residues: 201.5448 Evaluate side-chains 147 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 1.797 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 3 residues processed: 26 average time/residue: 0.4576 time to fit residues: 18.1890 ------------------------------------------------------------------------------- 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: 8.9990 chunk 134 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 71 optimal weight: 0.0570 chunk 138 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 chunk 160 optimal weight: 50.0000 overall best weight: 2.6102 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4786 moved from start: 0.3099 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= 0.259 Angle : 0.684 7.923 27423 Z= 0.387 Chirality : 0.041 0.197 3068 Planarity : 0.007 0.123 2456 Dihedral : 29.843 177.253 4665 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.08 % Favored : 96.65 % Rotamer Outliers : 0.31 % 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: -0.53 (0.20), residues: 1524 helix: -0.03 (0.17), residues: 802 sheet: 1.15 (0.64), residues: 61 loop : -0.77 (0.24), residues: 661 *********************** 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 180 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 176 time to evaluate : 1.739 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 outliers start: 4 outliers final: 0 residues processed: 179 average time/residue: 0.3762 time to fit residues: 96.9816 Evaluate side-chains 110 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.800 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2309 ------------------------------------------------------------------------------- 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: 20.0000 chunk 109 optimal weight: 40.0000 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 173 optimal weight: 50.0000 chunk 143 optimal weight: 20.0000 chunk 159 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5025 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 19359 Z= 0.343 Angle : 0.680 7.750 27423 Z= 0.389 Chirality : 0.040 0.172 3068 Planarity : 0.006 0.076 2456 Dihedral : 30.104 177.196 4665 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.22 % Favored : 96.52 % Rotamer Outliers : 0.31 % 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: 0.11 (0.21), residues: 1524 helix: 0.54 (0.18), residues: 806 sheet: 1.23 (0.60), residues: 72 loop : -0.55 (0.24), residues: 646 *********************** 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 153 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 1.757 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 outliers start: 4 outliers final: 0 residues processed: 152 average time/residue: 0.3830 time to fit residues: 83.5570 Evaluate side-chains 95 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.742 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1475 ------------------------------------------------------------------------------- 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: 10.0000 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: 5.9990 chunk 153 optimal weight: 0.0770 chunk 46 optimal weight: 0.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- 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 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 469 GLN ** K 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5000 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 19359 Z= 0.238 Angle : 0.600 8.125 27423 Z= 0.342 Chirality : 0.038 0.178 3068 Planarity : 0.005 0.094 2456 Dihedral : 30.102 177.667 4665 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.08 % Favored : 96.72 % Rotamer Outliers : 0.08 % 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: 0.60 (0.21), residues: 1524 helix: 0.99 (0.18), residues: 814 sheet: 1.46 (0.61), residues: 72 loop : -0.41 (0.25), residues: 638 *********************** 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 135 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.864 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 outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.3739 time to fit residues: 73.2376 Evaluate side-chains 98 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.828 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1093 ------------------------------------------------------------------------------- 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: 5.9990 chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 127 optimal weight: 30.0000 chunk 70 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 112 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5134 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 19359 Z= 0.340 Angle : 0.645 7.589 27423 Z= 0.367 Chirality : 0.040 0.195 3068 Planarity : 0.005 0.067 2456 Dihedral : 30.213 176.858 4665 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.54 % Favored : 96.26 % Rotamer Outliers : 0.00 % 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: 1.13 (0.18), residues: 804 sheet: 1.72 (0.62), residues: 72 loop : -0.37 (0.24), residues: 648 *********************** 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 121 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3405 time to fit residues: 62.7219 Evaluate side-chains 82 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.788 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1664 ------------------------------------------------------------------------------- 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: 50.0000 chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 171 optimal weight: 50.0000 chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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** ** 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: 0.5052 moved from start: 0.6374 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= 0.206 Angle : 0.580 8.836 27423 Z= 0.331 Chirality : 0.037 0.156 3068 Planarity : 0.004 0.064 2456 Dihedral : 30.178 178.146 4665 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.76 % Favored : 97.11 % Rotamer Outliers : 0.00 % 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: 0.97 (0.22), residues: 1524 helix: 1.31 (0.18), residues: 805 sheet: 1.61 (0.61), residues: 72 loop : -0.24 (0.25), residues: 647 *********************** 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 123 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.3663 time to fit residues: 67.4383 Evaluate side-chains 82 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.744 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2108 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 95 optimal weight: 7.9990 chunk 170 optimal weight: 30.0000 chunk 106 optimal weight: 10.0000 chunk 104 optimal weight: 50.0000 chunk 78 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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** K 572 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5246 moved from start: 0.7257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.079 19359 Z= 0.456 Angle : 0.713 8.555 27423 Z= 0.406 Chirality : 0.042 0.153 3068 Planarity : 0.005 0.064 2456 Dihedral : 30.452 176.866 4665 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 24.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.61 % Favored : 96.26 % Rotamer Outliers : 0.00 % 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: 0.49 (0.21), residues: 1524 helix: 0.86 (0.18), residues: 802 sheet: 1.48 (0.60), residues: 72 loop : -0.40 (0.25), residues: 650 *********************** 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 101 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.3764 time to fit residues: 56.8951 Evaluate side-chains 75 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.739 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1436 ------------------------------------------------------------------------------- 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: 20.0000 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 116 optimal weight: 0.0670 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** 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** K 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5078 moved from start: 0.7181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 19359 Z= 0.183 Angle : 0.590 9.754 27423 Z= 0.333 Chirality : 0.038 0.180 3068 Planarity : 0.004 0.061 2456 Dihedral : 30.338 178.646 4665 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.82 % Favored : 97.05 % Rotamer Outliers : 0.00 % 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: 0.92 (0.22), residues: 1524 helix: 1.29 (0.18), residues: 801 sheet: 1.45 (0.60), residues: 72 loop : -0.27 (0.25), residues: 651 *********************** 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 112 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.751 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 outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.3457 time to fit residues: 59.2264 Evaluate side-chains 84 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.693 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1418 ------------------------------------------------------------------------------- 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: 9.9990 chunk 149 optimal weight: 40.0000 chunk 158 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 124 optimal weight: 50.0000 chunk 48 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 104 optimal weight: 50.0000 chunk 168 optimal weight: 7.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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** K 539 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5187 moved from start: 0.7589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 19359 Z= 0.343 Angle : 0.635 9.164 27423 Z= 0.361 Chirality : 0.039 0.164 3068 Planarity : 0.005 0.061 2456 Dihedral : 30.347 177.831 4665 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer Outliers : 0.00 % 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: 0.78 (0.22), residues: 1524 helix: 1.13 (0.18), residues: 797 sheet: 1.50 (0.59), residues: 71 loop : -0.28 (0.25), residues: 656 *********************** 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 94 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.793 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 outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.3383 time to fit residues: 49.1477 Evaluate side-chains 73 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.647 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0823 ------------------------------------------------------------------------------- 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: 3.9990 chunk 79 optimal weight: 6.9990 chunk 116 optimal weight: 0.0980 chunk 176 optimal weight: 20.0000 chunk 162 optimal weight: 0.4980 chunk 140 optimal weight: 40.0000 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 30.0000 chunk 86 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 149 optimal weight: 50.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5082 moved from start: 0.7619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19359 Z= 0.192 Angle : 0.595 10.408 27423 Z= 0.334 Chirality : 0.038 0.165 3068 Planarity : 0.004 0.059 2456 Dihedral : 30.220 178.861 4665 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.62 % Favored : 97.24 % Rotamer Outliers : 0.00 % 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: 0.97 (0.22), residues: 1524 helix: 1.30 (0.18), residues: 801 sheet: 1.43 (0.58), residues: 71 loop : -0.20 (0.25), residues: 652 ********************** 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 109 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3390 time to fit residues: 57.0968 Evaluate side-chains 89 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.815 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2429 ------------------------------------------------------------------------------- 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: 5.9990 chunk 129 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.059239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.024620 restraints weight = 154351.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.025306 restraints weight = 82604.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.025702 restraints weight = 57712.708| |-----------------------------------------------------------------------------| r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.7787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 19359 Z= 0.238 Angle : 0.588 9.849 27423 Z= 0.333 Chirality : 0.037 0.164 3068 Planarity : 0.004 0.059 2456 Dihedral : 30.109 178.493 4665 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.89 % Favored : 96.98 % Rotamer Outliers : 0.00 % 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: 0.93 (0.22), residues: 1524 helix: 1.27 (0.18), residues: 799 sheet: 1.39 (0.58), residues: 71 loop : -0.21 (0.25), residues: 654 =============================================================================== Job complete usr+sys time: 3046.50 seconds wall clock time: 57 minutes 0.79 seconds (3420.79 seconds total)