Starting phenix.real_space_refine on Mon Dec 30 08:08:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y60_33630/12_2024/7y60_33630.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y60_33630/12_2024/7y60_33630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y60_33630/12_2024/7y60_33630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y60_33630/12_2024/7y60_33630.map" model { file = "/net/cci-nas-00/data/ceres_data/7y60_33630/12_2024/7y60_33630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y60_33630/12_2024/7y60_33630.cif" } resolution = 3.8 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1848 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 216 5.49 5 S 20 5.16 5 C 6418 2.51 5 N 2172 2.21 5 O 2552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11378 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "H" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 761 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "F" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 591 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 2198 Classifications: {'DNA': 108} Link IDs: {'rna3p': 107} Chain: "C" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 732 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "D" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 583 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "J" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 2230 Classifications: {'DNA': 108} Link IDs: {'rna3p': 107} Chain: "K" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 99 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "L" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 1749 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 13, 'TRANS': 340} Chain breaks: 4 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1113 Unresolved non-hydrogen angles: 1439 Unresolved non-hydrogen dihedrals: 949 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 18, 'TYR:plan': 13, 'ASN:plan1': 15, 'TRP:plan': 8, 'ASP:plan': 22, 'PHE:plan': 17, 'GLU:plan': 14, 'HIS:plan': 10} Unresolved non-hydrogen planarities: 600 Time building chain proxies: 6.94, per 1000 atoms: 0.61 Number of scatterers: 11378 At special positions: 0 Unit cell: (107, 116, 122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 216 15.00 O 2552 8.00 N 2172 7.00 C 6418 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 49.4% alpha, 15.4% beta 97 base pairs and 169 stacking pairs defined. Time for finding SS restraints: 5.13 Creating SS restraints... Processing helix chain 'G' and resid 63 through 79 Processing helix chain 'G' and resid 85 through 114 removed outlier: 3.786A pdb=" N ALA G 114 " --> pdb=" O CYS G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 132 removed outlier: 3.573A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 29 Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 49 through 77 removed outlier: 4.122A pdb=" N ARG H 55 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN H 64 " --> pdb=" O VAL H 60 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 65 " --> pdb=" O PHE H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.820A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.325A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.735A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.787A pdb=" N SER C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 77 removed outlier: 3.736A pdb=" N ASP C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 131 removed outlier: 3.502A pdb=" N ILE C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.761A pdb=" N ARG D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY D 56 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN D 64 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.736A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.505A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 4.054A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.703A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.201A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 703 through 707 removed outlier: 3.643A pdb=" N GLN K 706 " --> pdb=" O VAL K 703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.831A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 84 removed outlier: 6.917A pdb=" N ARG C 83 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'L' and resid 2 through 5 removed outlier: 6.881A pdb=" N PHE L 360 " --> pdb=" O TRP L 354 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TRP L 354 " --> pdb=" O PHE L 360 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA L 362 " --> pdb=" O ILE L 352 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE L 352 " --> pdb=" O ALA L 362 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER L 364 " --> pdb=" O SER L 350 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 16 through 21 removed outlier: 6.606A pdb=" N ALA L 35 " --> pdb=" O TYR L 17 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU L 19 " --> pdb=" O ALA L 33 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA L 33 " --> pdb=" O LEU L 19 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE L 21 " --> pdb=" O ARG L 31 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG L 31 " --> pdb=" O PHE L 21 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL L 41 " --> pdb=" O ASN L 61 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN L 61 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE L 43 " --> pdb=" O LEU L 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 69 through 74 removed outlier: 6.226A pdb=" N ILE L 90 " --> pdb=" O THR L 124 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR L 124 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU L 92 " --> pdb=" O VAL L 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 132 through 137 removed outlier: 6.220A pdb=" N ASP L 157 " --> pdb=" O LYS L 163 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS L 163 " --> pdb=" O ASP L 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 174 through 179 removed outlier: 3.617A pdb=" N GLY L 176 " --> pdb=" O LEU L 189 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU L 195 " --> pdb=" O ASN L 208 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN L 208 " --> pdb=" O LEU L 195 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL L 197 " --> pdb=" O ALA L 206 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG L 204 " --> pdb=" O SER L 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 211 through 213 Processing sheet with id=AB1, first strand: chain 'L' and resid 241 through 242 removed outlier: 3.822A pdb=" N ALA L 253 " --> pdb=" O THR L 265 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR L 265 " --> pdb=" O ALA L 253 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N CYS L 255 " --> pdb=" O MET L 263 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N MET L 263 " --> pdb=" O CYS L 255 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA L 279 " --> pdb=" O VAL L 268 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 288 through 299 removed outlier: 5.542A pdb=" N VAL L 318 " --> pdb=" O CYS L 294 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL L 296 " --> pdb=" O ARG L 316 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ARG L 316 " --> pdb=" O VAL L 296 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER L 326 " --> pdb=" O SER L 323 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 239 hydrogen bonds 438 hydrogen bond angles 0 basepair planarities 97 basepair parallelities 169 stacking parallelities Total time for adding SS restraints: 5.41 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2326 1.33 - 1.45: 3591 1.45 - 1.58: 5584 1.58 - 1.70: 430 1.70 - 1.82: 32 Bond restraints: 11963 Sorted by residual: bond pdb=" C ARG G 63 " pdb=" O ARG G 63 " ideal model delta sigma weight residual 1.234 1.210 0.025 1.20e-02 6.94e+03 4.27e+00 bond pdb=" N ARG G 63 " pdb=" CA ARG G 63 " ideal model delta sigma weight residual 1.456 1.479 -0.022 1.28e-02 6.10e+03 3.09e+00 bond pdb=" CD ARG G 63 " pdb=" NE ARG G 63 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.40e-02 5.10e+03 2.87e+00 bond pdb=" C LEU G 65 " pdb=" O LEU G 65 " ideal model delta sigma weight residual 1.244 1.229 0.014 9.80e-03 1.04e+04 2.17e+00 bond pdb=" C3' DC I 79 " pdb=" O3' DC I 79 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.05e+00 ... (remaining 11958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 16916 2.30 - 4.59: 173 4.59 - 6.89: 26 6.89 - 9.18: 7 9.18 - 11.48: 1 Bond angle restraints: 17123 Sorted by residual: angle pdb=" C LEU G 65 " pdb=" N PRO G 66 " pdb=" CA PRO G 66 " ideal model delta sigma weight residual 118.85 127.59 -8.74 1.09e+00 8.42e-01 6.44e+01 angle pdb=" N LYS G 64 " pdb=" CA LYS G 64 " pdb=" C LYS G 64 " ideal model delta sigma weight residual 111.28 119.29 -8.01 1.09e+00 8.42e-01 5.40e+01 angle pdb=" O3' DC I 84 " pdb=" C3' DC I 84 " pdb=" C2' DC I 84 " ideal model delta sigma weight residual 111.50 102.59 8.91 1.50e+00 4.44e-01 3.53e+01 angle pdb=" CA LEU G 65 " pdb=" C LEU G 65 " pdb=" N PRO G 66 " ideal model delta sigma weight residual 120.93 116.13 4.80 1.06e+00 8.90e-01 2.05e+01 angle pdb=" C ARG G 63 " pdb=" CA ARG G 63 " pdb=" CB ARG G 63 " ideal model delta sigma weight residual 109.90 116.83 -6.93 1.56e+00 4.11e-01 1.97e+01 ... (remaining 17118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 5462 35.09 - 70.17: 1123 70.17 - 105.26: 37 105.26 - 140.34: 0 140.34 - 175.43: 4 Dihedral angle restraints: 6626 sinusoidal: 3721 harmonic: 2905 Sorted by residual: dihedral pdb=" CA PHE K 711 " pdb=" C PHE K 711 " pdb=" N LEU K 712 " pdb=" CA LEU K 712 " ideal model delta harmonic sigma weight residual 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" C4' DC I 82 " pdb=" C3' DC I 82 " pdb=" O3' DC I 82 " pdb=" P DG I 83 " ideal model delta sinusoidal sigma weight residual 220.00 44.57 175.43 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC I 79 " pdb=" C3' DC I 79 " pdb=" O3' DC I 79 " pdb=" P DC I 80 " ideal model delta sinusoidal sigma weight residual -140.00 33.97 -173.97 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1657 0.049 - 0.097: 294 0.097 - 0.146: 66 0.146 - 0.194: 3 0.194 - 0.243: 1 Chirality restraints: 2021 Sorted by residual: chirality pdb=" CA LYS G 64 " pdb=" N LYS G 64 " pdb=" C LYS G 64 " pdb=" CB LYS G 64 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CG LEU F 37 " pdb=" CB LEU F 37 " pdb=" CD1 LEU F 37 " pdb=" CD2 LEU F 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" C3' DC I 84 " pdb=" C4' DC I 84 " pdb=" O3' DC I 84 " pdb=" C2' DC I 84 " both_signs ideal model delta sigma weight residual False -2.66 -2.82 0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 2018 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG G 63 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C ARG G 63 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG G 63 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS G 64 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 82 " -0.008 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C LEU G 82 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU G 82 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG G 83 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU G 65 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO G 66 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 66 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 66 " -0.021 5.00e-02 4.00e+02 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1111 2.74 - 3.28: 10944 3.28 - 3.82: 21860 3.82 - 4.36: 23489 4.36 - 4.90: 34819 Nonbonded interactions: 92223 Sorted by model distance: nonbonded pdb=" O2 DC I 56 " pdb=" N2 DG J 92 " model vdw 2.200 2.496 nonbonded pdb=" N2 DG I 37 " pdb=" O2 DC J 111 " model vdw 2.219 2.496 nonbonded pdb=" O2 DC I 54 " pdb=" N2 DG J 94 " model vdw 2.231 2.496 nonbonded pdb=" N2 DG I 67 " pdb=" O2 DC J 81 " model vdw 2.239 2.496 nonbonded pdb=" OG1 THR E 118 " pdb=" NH1 ARG F 45 " model vdw 2.240 3.120 ... (remaining 92218 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 59 through 134) selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 26 through 97) selection = (chain 'D' and resid 26 through 97) selection = (chain 'F' and resid 26 through 97) selection = (chain 'H' and resid 26 through 97) } 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.900 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 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 : 0.004 0.043 11963 Z= 0.210 Angle : 0.674 11.477 17123 Z= 0.397 Chirality : 0.040 0.243 2021 Planarity : 0.004 0.048 1458 Dihedral : 28.445 175.426 4730 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.30 % Allowed : 34.39 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.08 (0.26), residues: 974 helix: 0.66 (0.24), residues: 461 sheet: 0.40 (0.45), residues: 132 loop : -1.04 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 690 HIS 0.009 0.003 HIS C 113 PHE 0.022 0.001 PHE G 84 TYR 0.019 0.001 TYR C 99 ARG 0.014 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 236 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 LEU cc_start: 0.8749 (mt) cc_final: 0.8334 (mp) REVERT: F 88 TYR cc_start: 0.7381 (m-80) cc_final: 0.6741 (m-80) REVERT: D 68 ASP cc_start: 0.6511 (p0) cc_final: 0.5584 (p0) REVERT: D 77 LYS cc_start: 0.7997 (tptp) cc_final: 0.7789 (tppt) REVERT: A 90 MET cc_start: 0.8241 (mtm) cc_final: 0.7022 (mtm) outliers start: 7 outliers final: 0 residues processed: 239 average time/residue: 0.3186 time to fit residues: 100.2749 Evaluate side-chains 152 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 40.0000 chunk 87 optimal weight: 50.0000 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 105 optimal weight: 50.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 11963 Z= 0.455 Angle : 0.773 8.557 17123 Z= 0.441 Chirality : 0.045 0.201 2021 Planarity : 0.005 0.049 1458 Dihedral : 31.243 177.432 3422 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 25.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 8.55 % Allowed : 29.74 % Favored : 61.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.12 (0.26), residues: 974 helix: 0.74 (0.23), residues: 476 sheet: 0.58 (0.45), residues: 131 loop : -0.90 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 690 HIS 0.009 0.003 HIS G 113 PHE 0.027 0.002 PHE E 67 TYR 0.018 0.002 TYR C 99 ARG 0.008 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.915 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: H 26 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7687 (mm) REVERT: H 88 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: E 55 GLN cc_start: 0.7805 (tt0) cc_final: 0.7576 (tt0) REVERT: F 63 GLU cc_start: 0.6561 (tp30) cc_final: 0.6312 (tp30) REVERT: F 88 TYR cc_start: 0.7578 (m-80) cc_final: 0.7088 (m-80) REVERT: C 90 MET cc_start: 0.7708 (mmm) cc_final: 0.7461 (tpp) REVERT: C 94 GLU cc_start: 0.7612 (tp30) cc_final: 0.6902 (tp30) REVERT: D 77 LYS cc_start: 0.8200 (tptp) cc_final: 0.7975 (tppt) REVERT: A 90 MET cc_start: 0.7913 (mtm) cc_final: 0.7225 (mtm) outliers start: 46 outliers final: 26 residues processed: 209 average time/residue: 0.2802 time to fit residues: 78.9068 Evaluate side-chains 168 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 50.0000 chunk 114 optimal weight: 40.0000 chunk 93 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11963 Z= 0.237 Angle : 0.683 10.594 17123 Z= 0.386 Chirality : 0.041 0.175 2021 Planarity : 0.004 0.038 1458 Dihedral : 31.200 176.328 3422 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.39 % Allowed : 32.90 % Favored : 61.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.38 (0.26), residues: 974 helix: 0.97 (0.24), residues: 475 sheet: 0.48 (0.43), residues: 141 loop : -0.75 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 690 HIS 0.008 0.002 HIS C 113 PHE 0.015 0.002 PHE E 67 TYR 0.012 0.001 TYR H 88 ARG 0.009 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 1.050 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: G 63 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7685 (tpm170) REVERT: G 103 LEU cc_start: 0.8130 (tp) cc_final: 0.7866 (tt) REVERT: G 109 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8340 (tp) REVERT: H 77 LYS cc_start: 0.8880 (tptp) cc_final: 0.8449 (tptp) REVERT: H 88 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.7367 (m-80) REVERT: F 88 TYR cc_start: 0.7480 (m-80) cc_final: 0.6925 (m-80) REVERT: C 94 GLU cc_start: 0.7304 (tp30) cc_final: 0.6883 (tp30) REVERT: D 77 LYS cc_start: 0.8059 (tptp) cc_final: 0.7825 (tppt) REVERT: A 90 MET cc_start: 0.7770 (mtm) cc_final: 0.6920 (mtm) REVERT: B 64 ASN cc_start: 0.8895 (m-40) cc_final: 0.8323 (m110) outliers start: 29 outliers final: 14 residues processed: 191 average time/residue: 0.2623 time to fit residues: 68.4446 Evaluate side-chains 164 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 43 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.0970 chunk 79 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 105 optimal weight: 30.0000 chunk 112 optimal weight: 30.0000 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN C 55 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS A 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11963 Z= 0.225 Angle : 0.664 10.494 17123 Z= 0.379 Chirality : 0.041 0.264 2021 Planarity : 0.003 0.034 1458 Dihedral : 31.081 177.267 3422 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.76 % Allowed : 33.64 % Favored : 60.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.42 (0.27), residues: 974 helix: 0.94 (0.24), residues: 478 sheet: 0.68 (0.43), residues: 143 loop : -0.72 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 690 HIS 0.007 0.002 HIS C 113 PHE 0.011 0.001 PHE G 67 TYR 0.011 0.001 TYR C 99 ARG 0.008 0.001 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 1.022 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: G 103 LEU cc_start: 0.8122 (tp) cc_final: 0.7846 (tt) REVERT: H 88 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: F 88 TYR cc_start: 0.7462 (m-80) cc_final: 0.7066 (m-80) REVERT: D 77 LYS cc_start: 0.8086 (tptp) cc_final: 0.7840 (tppt) outliers start: 31 outliers final: 17 residues processed: 180 average time/residue: 0.2692 time to fit residues: 66.2627 Evaluate side-chains 162 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 30.0000 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 83 optimal weight: 0.0770 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 40.0000 chunk 77 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11963 Z= 0.267 Angle : 0.694 14.805 17123 Z= 0.390 Chirality : 0.041 0.266 2021 Planarity : 0.004 0.033 1458 Dihedral : 31.219 178.022 3422 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 6.13 % Allowed : 35.13 % Favored : 58.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.27), residues: 974 helix: 1.04 (0.24), residues: 475 sheet: 0.67 (0.43), residues: 146 loop : -0.62 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 690 HIS 0.006 0.001 HIS B 75 PHE 0.012 0.002 PHE G 67 TYR 0.011 0.001 TYR H 88 ARG 0.009 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 63 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7808 (tpm170) REVERT: G 103 LEU cc_start: 0.8176 (tp) cc_final: 0.7935 (tp) REVERT: H 88 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: E 64 LYS cc_start: 0.7936 (mmmm) cc_final: 0.7653 (mmmm) REVERT: F 84 MET cc_start: 0.7152 (tpp) cc_final: 0.6900 (tpp) REVERT: D 77 LYS cc_start: 0.8253 (tptp) cc_final: 0.8024 (tppt) outliers start: 33 outliers final: 19 residues processed: 178 average time/residue: 0.2835 time to fit residues: 68.3316 Evaluate side-chains 156 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 6.9990 chunk 100 optimal weight: 30.0000 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 112 optimal weight: 0.3980 chunk 93 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 108 optimal weight: 50.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11963 Z= 0.191 Angle : 0.665 11.951 17123 Z= 0.376 Chirality : 0.041 0.200 2021 Planarity : 0.003 0.029 1458 Dihedral : 30.990 176.918 3422 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.39 % Allowed : 37.92 % Favored : 56.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.51 (0.27), residues: 974 helix: 0.98 (0.24), residues: 477 sheet: 0.64 (0.43), residues: 148 loop : -0.59 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 690 HIS 0.008 0.001 HIS B 75 PHE 0.008 0.001 PHE E 78 TYR 0.015 0.001 TYR C 54 ARG 0.007 0.001 ARG D 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 1.069 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: G 63 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7650 (tpm170) REVERT: G 103 LEU cc_start: 0.8068 (tp) cc_final: 0.7785 (tp) REVERT: H 88 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: E 64 LYS cc_start: 0.7893 (mmmm) cc_final: 0.7553 (mmmm) REVERT: F 88 TYR cc_start: 0.7242 (m-80) cc_final: 0.6988 (m-80) REVERT: D 77 LYS cc_start: 0.8162 (tptp) cc_final: 0.7946 (tppt) outliers start: 29 outliers final: 12 residues processed: 181 average time/residue: 0.2716 time to fit residues: 66.6387 Evaluate side-chains 153 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 50.0000 chunk 94 optimal weight: 50.0000 chunk 62 optimal weight: 4.9990 chunk 111 optimal weight: 40.0000 chunk 69 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11963 Z= 0.356 Angle : 0.748 15.125 17123 Z= 0.419 Chirality : 0.044 0.294 2021 Planarity : 0.004 0.033 1458 Dihedral : 31.413 178.857 3422 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 24.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 6.32 % Allowed : 37.36 % Favored : 56.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.38 (0.27), residues: 974 helix: 0.74 (0.23), residues: 474 sheet: 0.82 (0.44), residues: 141 loop : -0.52 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 690 HIS 0.007 0.001 HIS B 75 PHE 0.031 0.002 PHE A 67 TYR 0.024 0.002 TYR F 72 ARG 0.011 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 1.004 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: G 63 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8139 (tpm170) REVERT: H 88 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.7424 (m-80) REVERT: F 88 TYR cc_start: 0.7423 (m-80) cc_final: 0.7068 (m-80) REVERT: D 77 LYS cc_start: 0.8281 (tptp) cc_final: 0.8068 (tppt) REVERT: B 72 TYR cc_start: 0.7734 (m-80) cc_final: 0.7157 (m-80) outliers start: 34 outliers final: 22 residues processed: 166 average time/residue: 0.2739 time to fit residues: 62.5252 Evaluate side-chains 153 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 40.0000 chunk 101 optimal weight: 0.0570 chunk 107 optimal weight: 40.0000 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 30.0000 overall best weight: 2.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11963 Z= 0.258 Angle : 0.722 14.521 17123 Z= 0.402 Chirality : 0.042 0.247 2021 Planarity : 0.004 0.032 1458 Dihedral : 31.367 176.740 3422 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.76 % Allowed : 37.17 % Favored : 57.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.27), residues: 974 helix: 0.70 (0.23), residues: 476 sheet: 0.83 (0.44), residues: 144 loop : -0.50 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 690 HIS 0.007 0.001 HIS B 75 PHE 0.029 0.002 PHE A 67 TYR 0.012 0.001 TYR B 88 ARG 0.006 0.001 ARG D 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 63 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7843 (tpm170) REVERT: H 88 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: E 55 GLN cc_start: 0.7538 (tt0) cc_final: 0.7318 (tt0) REVERT: F 88 TYR cc_start: 0.7309 (m-80) cc_final: 0.7098 (m-80) REVERT: C 120 MET cc_start: 0.7647 (mmm) cc_final: 0.7386 (mmt) REVERT: D 91 LYS cc_start: 0.7545 (mptt) cc_final: 0.7216 (tptt) REVERT: B 64 ASN cc_start: 0.8838 (m-40) cc_final: 0.8052 (m-40) outliers start: 31 outliers final: 21 residues processed: 164 average time/residue: 0.2664 time to fit residues: 61.1695 Evaluate side-chains 150 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.0370 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 81 optimal weight: 40.0000 chunk 31 optimal weight: 10.0000 chunk 94 optimal weight: 50.0000 chunk 98 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 overall best weight: 2.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11963 Z= 0.256 Angle : 0.776 17.807 17123 Z= 0.421 Chirality : 0.043 0.381 2021 Planarity : 0.004 0.071 1458 Dihedral : 31.362 177.654 3422 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.83 % Allowed : 39.22 % Favored : 55.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.22 (0.26), residues: 974 helix: 0.55 (0.23), residues: 475 sheet: 0.73 (0.43), residues: 146 loop : -0.51 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 690 HIS 0.007 0.001 HIS B 75 PHE 0.033 0.002 PHE A 67 TYR 0.012 0.001 TYR E 54 ARG 0.008 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 63 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8027 (tpm170) REVERT: H 88 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.7240 (m-80) REVERT: E 55 GLN cc_start: 0.7558 (tt0) cc_final: 0.7309 (tt0) REVERT: D 64 ASN cc_start: 0.7817 (p0) cc_final: 0.7491 (p0) REVERT: D 91 LYS cc_start: 0.7600 (mptt) cc_final: 0.7211 (tptt) outliers start: 26 outliers final: 22 residues processed: 154 average time/residue: 0.2767 time to fit residues: 58.3541 Evaluate side-chains 153 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.4980 chunk 76 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 106 optimal weight: 50.0000 chunk 92 optimal weight: 50.0000 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 98 optimal weight: 40.0000 chunk 28 optimal weight: 8.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 11963 Z= 0.368 Angle : 0.797 13.515 17123 Z= 0.445 Chirality : 0.045 0.387 2021 Planarity : 0.005 0.114 1458 Dihedral : 31.742 178.105 3422 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.46 % Allowed : 39.41 % Favored : 56.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 974 helix: 0.37 (0.23), residues: 475 sheet: 0.92 (0.45), residues: 134 loop : -0.50 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 690 HIS 0.007 0.002 HIS B 75 PHE 0.032 0.002 PHE A 67 TYR 0.015 0.002 TYR B 51 ARG 0.009 0.001 ARG B 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.967 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: G 63 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7818 (tpm170) REVERT: F 88 TYR cc_start: 0.7401 (m-80) cc_final: 0.7136 (m-80) REVERT: D 64 ASN cc_start: 0.7927 (p0) cc_final: 0.7503 (p0) REVERT: D 91 LYS cc_start: 0.7736 (mptt) cc_final: 0.7372 (tptt) outliers start: 24 outliers final: 20 residues processed: 150 average time/residue: 0.2779 time to fit residues: 56.5865 Evaluate side-chains 144 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 40.0000 chunk 38 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 50.0000 chunk 5 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.049059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.033414 restraints weight = 85059.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.034522 restraints weight = 45772.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.035233 restraints weight = 31104.714| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11963 Z= 0.248 Angle : 0.795 19.079 17123 Z= 0.428 Chirality : 0.044 0.379 2021 Planarity : 0.005 0.097 1458 Dihedral : 31.508 176.507 3422 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.09 % Allowed : 40.89 % Favored : 55.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.21 (0.27), residues: 974 helix: 0.55 (0.23), residues: 475 sheet: 0.72 (0.45), residues: 145 loop : -0.53 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 690 HIS 0.007 0.001 HIS B 75 PHE 0.010 0.002 PHE C 104 TYR 0.010 0.001 TYR F 72 ARG 0.009 0.001 ARG B 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2161.76 seconds wall clock time: 40 minutes 18.45 seconds (2418.45 seconds total)