Starting phenix.real_space_refine (version: dev) on Sat May 14 10:47:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/05_2022/6r25_4710_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/05_2022/6r25_4710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/05_2022/6r25_4710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/05_2022/6r25_4710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/05_2022/6r25_4710_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/05_2022/6r25_4710_updated.pdb" } resolution = 4.61 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped 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" Residue "A ARG 129": "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" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 18654 Number of models: 1 Model: "" Number of chains: 16 Chain: "K" Number of atoms: 5837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5837 Classifications: {'peptide': 737} Link IDs: {'PTRANS': 36, 'CIS': 1, 'TRANS': 698, 'PCIS': 1} 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: "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: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} 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: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 356 Unusual residues: {' ZN': 3, 'FAD': 1} Classifications: {'undetermined': 4, 'water': 300} Link IDs: {None: 303} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36 SG CYS K 53 55.670 53.110 19.749 1.00 48.02 S ATOM 69 SG CYS K 58 52.551 50.397 19.415 1.00 47.27 S ATOM 114 SG CYS K 65 49.904 64.512 19.360 1.00 37.13 S ATOM 173 SG CYS K 73 49.674 67.112 16.618 1.00 40.55 S ATOM 331 SG CYS K 92 53.559 65.891 17.690 1.00 37.37 S ATOM 354 SG CYS K 95 51.378 68.058 19.886 1.00 36.80 S ATOM 761 SG CYS K 142 25.258 54.078 23.619 1.00 35.45 S ATOM 799 SG CYS K 147 26.048 51.692 20.812 1.00 37.39 S ATOM 992 SG CYS K 169 27.431 55.303 20.820 1.00 34.97 S ATOM 1043 SG CYS K 185 23.515 54.522 20.136 1.00 38.56 S Time building chain proxies: 10.66, per 1000 atoms: 0.57 Number of scatterers: 18654 At special positions: 0 Unit cell: (134.62, 155.82, 118.72, 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 4292 8.00 N 3358 7.00 C 10651 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 16378 O5' DC J -20 .*. O " rejected from bonding due to valence issues. Atom "ATOM 16378 O5' DC J -20 .*. O " rejected from bonding due to valence issues. Atom "ATOM 16378 O5' DC J -20 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.63 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral 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 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 7 sheets defined 48.4% alpha, 4.7% beta 142 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 7.66 Creating SS restraints... 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: 3.674A 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: 3.627A pdb=" N VAL K 349 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU K 350 " --> pdb=" O GLN K 347 " (cutoff:3.500A) removed outlier: 3.553A 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: 5.055A 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: 3.616A 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 helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 78 removed outlier: 4.088A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.407A 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 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 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' 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: 3.725A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) 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: 6.870A 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: 6.835A 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: 8.553A pdb=" N ILE K 468 " --> pdb=" O PHE K 680 " (cutoff:3.500A) removed outlier: 6.331A 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: 3.896A 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: 6.757A pdb=" N THR K 611 " --> pdb=" O GLN K 599 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE K 601 " --> pdb=" O GLN K 609 " (cutoff:3.500A) removed outlier: 6.578A 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: 6.483A pdb=" N GLU K 89 " --> pdb=" O LEU K 85 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1452 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: 11.09 Time building geometry restraints manager: 9.25 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: 2381 1.31 - 1.44: 6614 1.44 - 1.57: 9642 1.57 - 1.69: 586 1.69 - 1.82: 81 Bond restraints: 19304 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 1.469 0.191 2.00e-02 2.50e+03 9.08e+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 8.02e+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 7.49e+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 5.18e+01 ... (remaining 19299 not shown) Histogram of bond angle deviations from ideal: 95.36 - 103.13: 701 103.13 - 110.90: 8173 110.90 - 118.67: 7905 118.67 - 126.44: 9607 126.44 - 134.21: 963 Bond angle restraints: 27349 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 117.23 108.24 8.99 1.36e+00 5.41e-01 4.37e+01 angle pdb=" O1P FAD K 901 " pdb=" P FAD K 901 " pdb=" O2P FAD K 901 " ideal model delta sigma weight residual 122.50 105.30 17.20 3.00e+00 1.11e-01 3.29e+01 angle pdb=" C ASP L 214 " pdb=" N PRO L 215 " pdb=" CA PRO L 215 " ideal model delta sigma weight residual 119.47 125.88 -6.41 1.16e+00 7.43e-01 3.05e+01 angle pdb=" CA ILE K 332 " pdb=" C ILE K 332 " pdb=" N PRO K 333 " ideal model delta sigma weight residual 120.83 117.59 3.24 5.90e-01 2.87e+00 3.02e+01 angle pdb=" CA LYS K 75 " pdb=" C LYS K 75 " pdb=" N ASN K 76 " ideal model delta sigma weight residual 119.98 115.34 4.64 8.50e-01 1.38e+00 2.98e+01 ... (remaining 27344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 8951 35.90 - 71.80: 1581 71.80 - 107.71: 31 107.71 - 143.61: 1 143.61 - 179.51: 1 Dihedral angle restraints: 10565 sinusoidal: 6089 harmonic: 4476 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 -66.86 66.86 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 -57.41 57.41 1 1.00e+01 1.00e-02 4.43e+01 ... (remaining 10562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2323 0.063 - 0.125: 615 0.125 - 0.188: 104 0.188 - 0.250: 14 0.250 - 0.313: 3 Chirality restraints: 3059 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 2.44e+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 1.84e+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 1.75e+00 ... (remaining 3056 not shown) Planarity restraints: 2447 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 " 0.139 2.00e-02 2.50e+03 pdb=" C2 FAD K 901 " -0.215 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 " -0.172 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 " 0.149 2.00e-02 2.50e+03 pdb=" N1 FAD K 901 " -0.045 2.00e-02 2.50e+03 pdb=" N10 FAD K 901 " 0.261 2.00e-02 2.50e+03 pdb=" N3 FAD K 901 " -0.223 2.00e-02 2.50e+03 pdb=" N5 FAD K 901 " 0.370 2.00e-02 2.50e+03 pdb=" O2 FAD K 901 " -0.371 2.00e-02 2.50e+03 pdb=" O4 FAD K 901 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 40 " -1.098 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 " 0.012 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 " 1.006 9.50e-02 1.11e+02 4.51e-01 1.23e+02 pdb=" NE ARG G 11 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG G 11 " -0.011 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 2444 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 12 1.81 - 2.58: 205 2.58 - 3.35: 23312 3.35 - 4.13: 55510 4.13 - 4.90: 85280 Nonbonded interactions: 164319 Sorted by model distance: nonbonded pdb=" CB GLN M 19 " pdb=" O5' DC J -20 " model vdw 1.036 3.440 nonbonded pdb=" OE1 GLN M 19 " pdb=" OP2 DC J -20 " model vdw 1.301 3.040 nonbonded pdb=" CG GLN M 19 " pdb=" O5' DC J -20 " model vdw 1.349 3.440 nonbonded pdb=" CD GLN M 19 " pdb=" OP2 DC J -20 " model vdw 1.474 3.270 nonbonded pdb=" O HIS E 39 " pdb=" O ARG E 40 " model vdw 1.497 3.040 ... (remaining 164314 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' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 17 through 120) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 25 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 10651 2.51 5 N 3358 2.21 5 O 4292 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.990 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: 7.000 Check model and map are aligned: 0.260 Convert atoms to be neutral: 0.160 Process input model: 62.000 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4457 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 19304 Z= 0.503 Angle : 1.047 17.201 27349 Z= 0.637 Chirality : 0.058 0.313 3059 Planarity : 0.023 0.492 2447 Dihedral : 25.567 179.511 7681 Min Nonbonded Distance : 1.036 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 1.32 % Allowed : 4.87 % Favored : 93.81 % Rotamer Outliers : 5.67 % 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: -2.97 (0.18), residues: 1518 helix: -2.25 (0.14), residues: 782 sheet: 0.51 (0.69), residues: 61 loop : -1.69 (0.21), residues: 675 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 215 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 14 residues processed: 282 average time/residue: 0.4372 time to fit residues: 166.8079 Evaluate side-chains 112 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.691 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3077 time to fit residues: 8.6815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 50.0000 chunk 137 optimal weight: 6.9990 chunk 53 optimal weight: 30.0000 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 76 ASN K 93 ASN K 98 HIS K 400 GLN K 440 ASN L 218 HIS M 19 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4664 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 19304 Z= 0.317 Angle : 0.703 9.968 27349 Z= 0.398 Chirality : 0.041 0.171 3059 Planarity : 0.006 0.067 2447 Dihedral : 29.973 179.143 4657 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.49 % Favored : 96.31 % 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: -0.33 (0.21), residues: 1518 helix: 0.16 (0.17), residues: 800 sheet: 1.15 (0.64), residues: 61 loop : -0.71 (0.24), residues: 657 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 1.742 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 outliers start: 4 outliers final: 0 residues processed: 125 average time/residue: 0.4306 time to fit residues: 74.9066 Evaluate side-chains 74 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.561 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 54 optimal weight: 50.0000 chunk 128 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 469 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4695 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 19304 Z= 0.262 Angle : 0.634 9.506 27349 Z= 0.360 Chirality : 0.039 0.234 3059 Planarity : 0.005 0.056 2447 Dihedral : 30.123 177.943 4657 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.23 % Favored : 96.64 % 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: 0.47 (0.21), residues: 1518 helix: 0.92 (0.18), residues: 798 sheet: 1.39 (0.59), residues: 71 loop : -0.51 (0.24), residues: 649 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.4205 time to fit residues: 61.4514 Evaluate side-chains 70 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.679 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS G 68 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4930 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.073 19304 Z= 0.431 Angle : 0.737 8.331 27349 Z= 0.418 Chirality : 0.043 0.181 3059 Planarity : 0.006 0.062 2447 Dihedral : 30.723 172.999 4657 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 26.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.51 % Rotamer Outliers : 0.15 % 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: 0.33 (0.21), residues: 1518 helix: 0.67 (0.18), residues: 792 sheet: 1.66 (0.60), residues: 71 loop : -0.41 (0.24), residues: 655 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 1.673 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: 2 outliers final: 1 residues processed: 92 average time/residue: 0.4008 time to fit residues: 53.7036 Evaluate side-chains 60 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.845 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1721 time to fit residues: 2.6656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 40.0000 chunk 126 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 0 optimal weight: 90.0000 chunk 86 optimal weight: 0.0980 chunk 152 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 152 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 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: 0.4791 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 19304 Z= 0.215 Angle : 0.602 8.866 27349 Z= 0.340 Chirality : 0.038 0.216 3059 Planarity : 0.004 0.052 2447 Dihedral : 30.819 175.580 4657 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.17 % 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: 0.88 (0.22), residues: 1518 helix: 1.28 (0.18), residues: 792 sheet: 1.76 (0.60), residues: 71 loop : -0.35 (0.25), residues: 655 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.740 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 outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.4358 time to fit residues: 58.1932 Evaluate side-chains 61 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.856 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 7.9990 chunk 33 optimal weight: 40.0000 chunk 99 optimal weight: 10.0000 chunk 41 optimal weight: 0.0570 chunk 170 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 56 optimal weight: 50.0000 chunk 89 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 overall best weight: 5.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 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: 0.4873 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 19304 Z= 0.317 Angle : 0.628 8.203 27349 Z= 0.357 Chirality : 0.039 0.199 3059 Planarity : 0.005 0.054 2447 Dihedral : 30.785 175.591 4657 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.97 % 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: 0.94 (0.22), residues: 1518 helix: 1.29 (0.18), residues: 782 sheet: 1.78 (0.60), residues: 71 loop : -0.25 (0.25), residues: 665 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.817 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: 0 outliers final: 0 residues processed: 82 average time/residue: 0.4263 time to fit residues: 50.5128 Evaluate side-chains 54 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.768 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.3980 chunk 97 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4768 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 19304 Z= 0.186 Angle : 0.582 9.868 27349 Z= 0.328 Chirality : 0.038 0.210 3059 Planarity : 0.004 0.056 2447 Dihedral : 30.664 175.856 4657 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.97 % 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: 1.24 (0.22), residues: 1518 helix: 1.62 (0.19), residues: 784 sheet: 1.86 (0.61), residues: 71 loop : -0.22 (0.25), residues: 663 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.794 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: 85 average time/residue: 0.3866 time to fit residues: 48.6741 Evaluate side-chains 52 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.826 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 33 optimal weight: 50.0000 chunk 32 optimal weight: 40.0000 chunk 107 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 539 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4994 moved from start: 0.7031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.095 19304 Z= 0.476 Angle : 0.731 8.116 27349 Z= 0.417 Chirality : 0.043 0.179 3059 Planarity : 0.006 0.060 2447 Dihedral : 31.116 176.015 4657 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 30.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.56 % Favored : 96.38 % 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: 0.65 (0.21), residues: 1518 helix: 0.92 (0.18), residues: 785 sheet: 1.83 (0.60), residues: 71 loop : -0.22 (0.25), residues: 662 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.813 Fit side-chains 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: 73 average time/residue: 0.4309 time to fit residues: 46.6864 Evaluate side-chains 46 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.845 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 48 optimal weight: 50.0000 chunk 142 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4808 moved from start: 0.6845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 19304 Z= 0.198 Angle : 0.608 12.316 27349 Z= 0.338 Chirality : 0.039 0.276 3059 Planarity : 0.004 0.056 2447 Dihedral : 31.006 176.717 4657 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.71 % 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: 1.13 (0.22), residues: 1518 helix: 1.46 (0.19), residues: 785 sheet: 1.85 (0.60), residues: 71 loop : -0.18 (0.25), residues: 662 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.3472 time to fit residues: 41.3377 Evaluate side-chains 53 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 7.9990 chunk 102 optimal weight: 0.0270 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 139 optimal weight: 0.0000 chunk 14 optimal weight: 0.1980 chunk 107 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 overall best weight: 0.6444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 162 GLN C 73 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4723 moved from start: 0.6790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19304 Z= 0.164 Angle : 0.582 11.576 27349 Z= 0.324 Chirality : 0.038 0.268 3059 Planarity : 0.004 0.058 2447 Dihedral : 30.477 177.154 4657 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.04 % 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: 1.22 (0.22), residues: 1518 helix: 1.58 (0.19), residues: 782 sheet: 1.87 (0.59), residues: 71 loop : -0.19 (0.25), residues: 665 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.831 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: 82 average time/residue: 0.3547 time to fit residues: 44.5491 Evaluate side-chains 59 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 10.0000 chunk 42 optimal weight: 40.0000 chunk 128 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 50.0000 chunk 139 optimal weight: 20.0000 chunk 58 optimal weight: 0.3980 chunk 143 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 122 optimal weight: 0.0170 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 440 ASN K 572 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.095678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.053658 restraints weight = 233115.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.047843 restraints weight = 172808.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.045315 restraints weight = 106647.762| |-----------------------------------------------------------------------------| r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.6831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 19304 Z= 0.162 Angle : 0.579 11.121 27349 Z= 0.323 Chirality : 0.037 0.244 3059 Planarity : 0.005 0.109 2447 Dihedral : 30.222 178.223 4657 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.23 % 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: 1.14 (0.22), residues: 1518 helix: 1.48 (0.19), residues: 785 sheet: 1.88 (0.59), residues: 71 loop : -0.18 (0.25), residues: 662 =============================================================================== Job complete usr+sys time: 3411.25 seconds wall clock time: 63 minutes 13.23 seconds (3793.23 seconds total)