Starting phenix.real_space_refine on Sat Feb 17 12:22:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/02_2024/6r25_4710_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/02_2024/6r25_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_4710/02_2024/6r25_4710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/02_2024/6r25_4710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/02_2024/6r25_4710_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r25_4710/02_2024/6r25_4710_updated.pdb" } resolution = 4.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 296 5.49 5 S 54 5.16 5 C 10651 2.51 5 N 3358 2.21 5 O 4292 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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-5238/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: {'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: "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: 10.10, per 1000 atoms: 0.54 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: 9.85 Conformation dependent library (CDL) restraints added in 2.5 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 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: 10.04 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: 14.02 Time building geometry restraints manager: 10.29 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: 9204 35.90 - 71.80: 1631 71.80 - 107.71: 31 107.71 - 143.61: 1 143.61 - 179.51: 1 Dihedral angle restraints: 10868 sinusoidal: 6392 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 10865 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 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.580 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 71.010 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4527 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 : 25.638 179.511 7984 Min Nonbonded Distance : 1.036 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 1.32 % Allowed : 4.87 % Favored : 93.81 % Rotamer: Outliers : 5.67 % Allowed : 4.68 % Favored : 89.65 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 117 HIS 0.014 0.002 HIS B 75 PHE 0.033 0.003 PHE C 25 TYR 0.018 0.003 TYR K 767 ARG 0.016 0.001 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 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 : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 119 SER cc_start: 0.1979 (OUTLIER) cc_final: 0.1571 (t) REVERT: K 230 MET cc_start: 0.5295 (mtm) cc_final: 0.4207 (ttt) REVERT: K 265 MET cc_start: -0.0069 (ttm) cc_final: -0.0396 (tpp) REVERT: K 267 ARG cc_start: 0.4737 (OUTLIER) cc_final: 0.4250 (mpp-170) REVERT: K 458 MET cc_start: -0.1116 (mtm) cc_final: -0.1592 (mtt) REVERT: M 4 MET cc_start: -0.5283 (tpp) cc_final: -0.5670 (tpt) REVERT: M 18 LYS cc_start: 0.0005 (OUTLIER) cc_final: -0.0263 (pttt) REVERT: D 38 VAL cc_start: 0.9645 (t) cc_final: 0.9423 (m) REVERT: E 65 LEU cc_start: 0.8813 (mt) cc_final: 0.8353 (mt) REVERT: F 25 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8090 (t0) REVERT: F 62 LEU cc_start: 0.9357 (mt) cc_final: 0.8943 (tt) REVERT: G 72 ASP cc_start: 0.8589 (m-30) cc_final: 0.8368 (p0) REVERT: G 112 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8071 (mm-40) outliers start: 74 outliers final: 14 residues processed: 282 average time/residue: 0.4603 time to fit residues: 173.9583 Evaluate side-chains 118 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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: 8.9990 chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 30.0000 chunk 45 optimal weight: 7.9990 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: 20.0000 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 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 ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4751 moved from start: 0.3210 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= 0.328 Angle : 0.713 9.886 27349 Z= 0.404 Chirality : 0.042 0.232 3059 Planarity : 0.006 0.077 2447 Dihedral : 29.565 179.757 4960 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.29 % Favored : 96.51 % Rotamer: Outliers : 0.23 % Allowed : 1.92 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1518 helix: 0.22 (0.17), residues: 797 sheet: 1.16 (0.64), residues: 61 loop : -0.79 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 201 HIS 0.008 0.002 HIS A 113 PHE 0.023 0.002 PHE C 25 TYR 0.020 0.002 TYR D 37 ARG 0.012 0.001 ARG K 51 *********************** 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 129 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.582 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: K 171 MET cc_start: -0.4045 (ttp) cc_final: -0.6304 (mtm) REVERT: K 230 MET cc_start: 0.4876 (mtm) cc_final: 0.4025 (ttt) REVERT: K 458 MET cc_start: -0.0868 (mtm) cc_final: -0.1592 (mtt) REVERT: M 4 MET cc_start: -0.5335 (tpp) cc_final: -0.5558 (tpt) REVERT: D 103 LEU cc_start: 0.9132 (pt) cc_final: 0.8920 (pt) REVERT: E 124 ILE cc_start: 0.9451 (mt) cc_final: 0.9221 (mm) REVERT: H 59 MET cc_start: 0.8395 (tpt) cc_final: 0.7944 (tpp) outliers start: 3 outliers final: 0 residues processed: 127 average time/residue: 0.4393 time to fit residues: 77.1903 Evaluate side-chains 71 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.714 ------------------------------------------------------------------------------- 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: 5.9990 chunk 49 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 44 optimal weight: 50.0000 chunk 160 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 54 optimal weight: 50.0000 chunk 128 optimal weight: 0.0870 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 440 ASN ** 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** G 68 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4818 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 19304 Z= 0.293 Angle : 0.653 9.221 27349 Z= 0.371 Chirality : 0.040 0.241 3059 Planarity : 0.005 0.080 2447 Dihedral : 29.789 176.368 4960 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.16 % Favored : 96.71 % Rotamer: Outliers : 0.08 % Allowed : 3.07 % Favored : 96.86 % 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: 0.54 (0.21), residues: 1518 helix: 0.99 (0.18), residues: 793 sheet: 1.46 (0.59), residues: 71 loop : -0.49 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 762 HIS 0.010 0.002 HIS E 39 PHE 0.014 0.001 PHE K 91 TYR 0.021 0.002 TYR A 54 ARG 0.010 0.001 ARG C 20 *********************** 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 98 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.777 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: K 171 MET cc_start: -0.4144 (ttp) cc_final: -0.6006 (mtm) REVERT: K 230 MET cc_start: 0.5223 (mtm) cc_final: 0.4202 (ttt) REVERT: K 458 MET cc_start: -0.1059 (mtm) cc_final: -0.1594 (mtt) REVERT: M 4 MET cc_start: -0.5204 (tpp) cc_final: -0.5424 (tpt) REVERT: H 59 MET cc_start: 0.8418 (tpt) cc_final: 0.7978 (tpp) REVERT: H 73 GLU cc_start: 0.8100 (tp30) cc_final: 0.7864 (tp30) outliers start: 1 outliers final: 1 residues processed: 97 average time/residue: 0.4474 time to fit residues: 61.2247 Evaluate side-chains 68 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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: 10.0000 chunk 17 optimal weight: 8.9990 chunk 76 optimal weight: 0.0670 chunk 107 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 overall best weight: 5.8126 ------------------------------------------------------------------------------- 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 ** F 25 ASN ** 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: 0.4952 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 19304 Z= 0.359 Angle : 0.670 8.242 27349 Z= 0.381 Chirality : 0.040 0.218 3059 Planarity : 0.005 0.056 2447 Dihedral : 30.028 171.897 4960 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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: 1518 helix: 0.94 (0.18), residues: 793 sheet: 1.67 (0.59), residues: 71 loop : -0.33 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 762 HIS 0.009 0.001 HIS F 75 PHE 0.023 0.001 PHE K 91 TYR 0.017 0.002 TYR E 54 ARG 0.025 0.001 ARG H 76 *********************** 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 87 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.756 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: K 171 MET cc_start: -0.4397 (ttp) cc_final: -0.6110 (mtm) REVERT: K 230 MET cc_start: 0.5446 (mtm) cc_final: 0.4209 (ttt) REVERT: K 458 MET cc_start: -0.1159 (mtm) cc_final: -0.1715 (mtt) REVERT: M 4 MET cc_start: -0.5077 (tpp) cc_final: -0.5473 (tpt) REVERT: A 120 MET cc_start: 0.8032 (mmp) cc_final: 0.7791 (mmm) REVERT: H 59 MET cc_start: 0.8360 (tpt) cc_final: 0.7898 (tpp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.4363 time to fit residues: 54.2208 Evaluate side-chains 62 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.831 ------------------------------------------------------------------------------- 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: 3.9990 chunk 2 optimal weight: 50.0000 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 145 optimal weight: 0.0970 chunk 117 optimal weight: 7.9990 chunk 0 optimal weight: 90.0000 chunk 86 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 152 GLN ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** 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: 0.4895 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19304 Z= 0.256 Angle : 0.604 11.242 27349 Z= 0.344 Chirality : 0.038 0.144 3059 Planarity : 0.004 0.060 2447 Dihedral : 30.167 174.559 4960 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: 1.00 (0.22), residues: 1518 helix: 1.39 (0.18), residues: 787 sheet: 1.81 (0.60), residues: 71 loop : -0.29 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 762 HIS 0.006 0.001 HIS F 75 PHE 0.013 0.001 PHE K 91 TYR 0.013 0.001 TYR B 88 ARG 0.005 0.001 ARG C 20 *********************** 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 87 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.906 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: K 171 MET cc_start: -0.4303 (ttp) cc_final: -0.6029 (mtm) REVERT: K 230 MET cc_start: 0.5377 (mtm) cc_final: 0.4177 (ttt) REVERT: M 4 MET cc_start: -0.5069 (tpp) cc_final: -0.5503 (tpt) REVERT: H 59 MET cc_start: 0.8336 (tpt) cc_final: 0.7750 (tpp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.4107 time to fit residues: 51.6149 Evaluate side-chains 58 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.721 ------------------------------------------------------------------------------- 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: 50.0000 chunk 99 optimal weight: 8.9990 chunk 41 optimal weight: 0.0060 chunk 170 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 40.0000 chunk 56 optimal weight: 50.0000 chunk 89 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 162 GLN ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** 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: 0.4939 moved from start: 0.6092 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= 0.297 Angle : 0.614 10.412 27349 Z= 0.350 Chirality : 0.038 0.145 3059 Planarity : 0.004 0.051 2447 Dihedral : 30.180 174.145 4960 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 1.08 (0.22), residues: 1518 helix: 1.42 (0.18), residues: 786 sheet: 1.81 (0.60), residues: 71 loop : -0.21 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.010 0.001 HIS F 75 PHE 0.014 0.001 PHE B 61 TYR 0.014 0.001 TYR E 99 ARG 0.006 0.001 ARG K 285 *********************** 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 86 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.632 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: K 171 MET cc_start: -0.4298 (ttp) cc_final: -0.6063 (mtm) REVERT: K 230 MET cc_start: 0.5348 (mtm) cc_final: 0.4166 (ttt) REVERT: M 4 MET cc_start: -0.5117 (tpp) cc_final: -0.5496 (tpt) REVERT: E 124 ILE cc_start: 0.9228 (mt) cc_final: 0.8983 (mm) REVERT: H 59 MET cc_start: 0.8168 (tpt) cc_final: 0.7710 (tpt) REVERT: H 97 LEU cc_start: 0.9386 (mt) cc_final: 0.9185 (mt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.4013 time to fit residues: 49.9817 Evaluate side-chains 56 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.859 ------------------------------------------------------------------------------- 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: 10.0000 chunk 97 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 104 optimal weight: 0.0170 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 152 GLN K 440 ASN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 572 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4823 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19304 Z= 0.175 Angle : 0.574 9.934 27349 Z= 0.323 Chirality : 0.037 0.146 3059 Planarity : 0.004 0.055 2447 Dihedral : 29.991 175.163 4960 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: 1.32 (0.22), residues: 1518 helix: 1.64 (0.19), residues: 788 sheet: 1.85 (0.61), residues: 71 loop : -0.12 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.004 0.001 HIS F 75 PHE 0.014 0.001 PHE K 91 TYR 0.013 0.001 TYR C 50 ARG 0.004 0.000 ARG H 89 *********************** 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 : 1.787 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: K 171 MET cc_start: -0.4363 (ttp) cc_final: -0.6072 (mtm) REVERT: K 230 MET cc_start: 0.5278 (mtm) cc_final: 0.4170 (ttt) REVERT: M 4 MET cc_start: -0.5191 (tpp) cc_final: -0.5489 (tpt) REVERT: G 91 GLU cc_start: 0.7807 (pm20) cc_final: 0.7494 (pm20) REVERT: H 59 MET cc_start: 0.8153 (tpt) cc_final: 0.7733 (tpp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.4168 time to fit residues: 52.8060 Evaluate side-chains 58 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.765 ------------------------------------------------------------------------------- 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: 0.0870 chunk 51 optimal weight: 50.0000 chunk 33 optimal weight: 50.0000 chunk 32 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 overall best weight: 5.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 152 GLN K 539 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS F 25 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4962 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 19304 Z= 0.327 Angle : 0.625 9.186 27349 Z= 0.355 Chirality : 0.038 0.147 3059 Planarity : 0.005 0.062 2447 Dihedral : 30.149 176.416 4960 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 1.12 (0.22), residues: 1518 helix: 1.43 (0.19), residues: 786 sheet: 1.79 (0.60), residues: 71 loop : -0.13 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.008 0.001 HIS F 75 PHE 0.015 0.001 PHE E 104 TYR 0.015 0.001 TYR B 88 ARG 0.005 0.001 ARG A 40 *********************** 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 81 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.683 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: K 171 MET cc_start: -0.4368 (ttp) cc_final: -0.6056 (mtm) REVERT: K 230 MET cc_start: 0.5336 (mtm) cc_final: 0.4149 (ttt) REVERT: M 4 MET cc_start: -0.5223 (tpp) cc_final: -0.5561 (tpt) REVERT: H 59 MET cc_start: 0.8270 (tpt) cc_final: 0.7661 (tpt) REVERT: H 97 LEU cc_start: 0.9448 (mt) cc_final: 0.9236 (mt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.4054 time to fit residues: 47.7583 Evaluate side-chains 54 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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: 10.0000 chunk 148 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 68 optimal weight: 50.0000 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 50.0000 chunk 142 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 184 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** 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: 0.4865 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19304 Z= 0.190 Angle : 0.587 10.689 27349 Z= 0.328 Chirality : 0.037 0.153 3059 Planarity : 0.004 0.063 2447 Dihedral : 30.101 177.615 4960 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 1.29 (0.22), residues: 1518 helix: 1.61 (0.19), residues: 787 sheet: 1.80 (0.60), residues: 71 loop : -0.11 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.005 0.001 HIS F 75 PHE 0.011 0.001 PHE K 91 TYR 0.015 0.001 TYR F 88 ARG 0.009 0.000 ARG H 69 *********************** 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 81 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 171 MET cc_start: -0.4372 (ttp) cc_final: -0.6052 (mtm) REVERT: K 230 MET cc_start: 0.5406 (mtm) cc_final: 0.4154 (ttt) REVERT: M 4 MET cc_start: -0.5235 (tpp) cc_final: -0.5566 (tpt) REVERT: G 91 GLU cc_start: 0.7598 (pm20) cc_final: 0.7315 (pm20) REVERT: H 59 MET cc_start: 0.8198 (tpt) cc_final: 0.7583 (tpt) REVERT: H 97 LEU cc_start: 0.9332 (mt) cc_final: 0.9113 (mt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.3759 time to fit residues: 44.8655 Evaluate side-chains 56 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.655 ------------------------------------------------------------------------------- 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: 20.0000 chunk 79 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 139 optimal weight: 0.0370 chunk 14 optimal weight: 40.0000 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 overall best weight: 2.4062 ------------------------------------------------------------------------------- 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** F 25 ASN ** 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: 0.4859 moved from start: 0.6741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19304 Z= 0.199 Angle : 0.576 10.529 27349 Z= 0.322 Chirality : 0.037 0.146 3059 Planarity : 0.004 0.063 2447 Dihedral : 29.867 178.065 4960 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 1.32 (0.22), residues: 1518 helix: 1.65 (0.19), residues: 785 sheet: 1.86 (0.60), residues: 71 loop : -0.11 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 762 HIS 0.006 0.001 HIS F 75 PHE 0.011 0.001 PHE K 91 TYR 0.019 0.001 TYR F 88 ARG 0.005 0.000 ARG H 76 ********************** 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 79 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 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: K 171 MET cc_start: -0.4578 (ttp) cc_final: -0.6156 (mtm) REVERT: K 230 MET cc_start: 0.5376 (mtm) cc_final: 0.4014 (ttt) REVERT: M 4 MET cc_start: -0.5239 (tpp) cc_final: -0.5567 (tpt) REVERT: F 59 LYS cc_start: 0.8998 (ptpp) cc_final: 0.8793 (pttm) REVERT: G 91 GLU cc_start: 0.7479 (pm20) cc_final: 0.7202 (pm20) REVERT: H 59 MET cc_start: 0.8217 (tpt) cc_final: 0.7798 (tpp) REVERT: H 97 LEU cc_start: 0.9371 (mt) cc_final: 0.9133 (mt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.4012 time to fit residues: 46.9609 Evaluate side-chains 57 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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: 4.9990 chunk 20 optimal weight: 30.0000 chunk 38 optimal weight: 40.0000 chunk 139 optimal weight: 9.9990 chunk 58 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 122 optimal weight: 0.1980 overall best weight: 7.0390 ------------------------------------------------------------------------------- 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** F 25 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 81 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 = 0.3547 r_free = 0.3547 target = 0.089439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.044158 restraints weight = 243669.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.044622 restraints weight = 196873.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.041951 restraints weight = 179692.627| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.7436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 19304 Z= 0.409 Angle : 0.693 9.077 27349 Z= 0.392 Chirality : 0.041 0.167 3059 Planarity : 0.006 0.053 2447 Dihedral : 30.405 178.698 4960 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 27.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.49 % Favored : 96.44 % Rotamer: Outliers : 0.08 % Allowed : 0.38 % Favored : 99.54 % 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: 0.90 (0.22), residues: 1518 helix: 1.13 (0.18), residues: 784 sheet: 1.91 (0.61), residues: 71 loop : -0.10 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.008 0.001 HIS F 75 PHE 0.020 0.002 PHE B 61 TYR 0.024 0.002 TYR F 88 ARG 0.010 0.001 ARG H 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3416.77 seconds wall clock time: 63 minutes 41.87 seconds (3821.87 seconds total)