Starting phenix.real_space_refine on Mon Dec 30 23:18:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sn9_40617/12_2024/8sn9_40617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sn9_40617/12_2024/8sn9_40617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sn9_40617/12_2024/8sn9_40617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sn9_40617/12_2024/8sn9_40617.map" model { file = "/net/cci-nas-00/data/ceres_data/8sn9_40617/12_2024/8sn9_40617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sn9_40617/12_2024/8sn9_40617.cif" } resolution = 3.9 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= 0.004 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 2 6.06 5 P 294 5.49 5 S 33 5.16 5 C 8264 2.51 5 N 2710 2.21 5 O 3288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14591 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 682 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 53.370 71.554 45.709 1.00 90.47 S ATOM 12446 SG CYS K 51 52.485 67.970 44.923 1.00 88.01 S ATOM 12470 SG CYS K 54 52.408 70.634 42.129 1.00 89.07 S ATOM 12187 SG CYS K 16 43.387 65.421 52.089 1.00 95.41 S ATOM 12205 SG CYS K 19 43.026 62.019 53.804 1.00 88.88 S ATOM 12335 SG CYS K 36 44.943 64.767 55.368 1.00 85.82 S ATOM 12357 SG CYS K 39 46.383 62.853 52.270 1.00 90.71 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 residue: pdb=" N GLY M 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY M 76 " occ=0.25 Time building chain proxies: 8.86, per 1000 atoms: 0.61 Number of scatterers: 14591 At special positions: 0 Unit cell: (130.144, 130.144, 124.832, 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 2 29.99 S 33 16.00 P 294 15.00 O 3288 8.00 N 2710 7.00 C 8264 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 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " Number of angles added : 9 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 13 sheets defined 61.6% alpha, 5.5% beta 136 base pairs and 252 stacking pairs defined. Time for finding SS restraints: 6.76 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.817A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.578A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.946A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.931A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.717A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.619A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.849A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.670A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.752A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.743A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.866A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.553A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.577A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 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: 3.893A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.782A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.811A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.550A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 Processing helix chain 'K' and resid 58 through 68 removed outlier: 3.806A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 91 Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 86 through 91 removed outlier: 4.081A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.591A pdb=" N ASP L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.652A pdb=" N ALA L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 146 removed outlier: 3.925A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.585A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.806A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.783A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.563A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.747A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16 492 hydrogen bonds defined for protein. 1453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 349 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 252 stacking parallelities Total time for adding SS restraints: 5.58 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3546 1.34 - 1.46: 4319 1.46 - 1.58: 6962 1.58 - 1.70: 586 1.70 - 1.82: 49 Bond restraints: 15462 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.08e+00 bond pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 1.523 1.502 0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" C3' DA J -73 " pdb=" C2' DA J -73 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" CB MET H 59 " pdb=" CG MET H 59 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.68e-01 ... (remaining 15457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 21543 1.53 - 3.07: 564 3.07 - 4.60: 31 4.60 - 6.13: 16 6.13 - 7.67: 2 Bond angle restraints: 22156 Sorted by residual: angle pdb=" CB MET H 59 " pdb=" CG MET H 59 " pdb=" SD MET H 59 " ideal model delta sigma weight residual 112.70 105.03 7.67 3.00e+00 1.11e-01 6.53e+00 angle pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 122.46 126.05 -3.59 1.41e+00 5.03e-01 6.47e+00 angle pdb=" C ALA L 19 " pdb=" N GLN L 20 " pdb=" CA GLN L 20 " ideal model delta sigma weight residual 121.54 126.31 -4.77 1.91e+00 2.74e-01 6.24e+00 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 118.86 -5.68 2.37e+00 1.78e-01 5.75e+00 angle pdb=" CG ARG L 15 " pdb=" CD ARG L 15 " pdb=" NE ARG L 15 " ideal model delta sigma weight residual 112.00 116.98 -4.98 2.20e+00 2.07e-01 5.12e+00 ... (remaining 22151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 7251 36.00 - 71.99: 1335 71.99 - 107.99: 14 107.99 - 143.99: 0 143.99 - 179.99: 2 Dihedral angle restraints: 8602 sinusoidal: 5466 harmonic: 3136 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 40.01 179.99 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 70.83 149.17 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CG ARG D 92 " pdb=" CD ARG D 92 " pdb=" NE ARG D 92 " pdb=" CZ ARG D 92 " ideal model delta sinusoidal sigma weight residual 180.00 135.58 44.42 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 8599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1768 0.032 - 0.064: 560 0.064 - 0.096: 131 0.096 - 0.128: 48 0.128 - 0.160: 7 Chirality restraints: 2514 Sorted by residual: chirality pdb=" CB VAL K 58 " pdb=" CA VAL K 58 " pdb=" CG1 VAL K 58 " pdb=" CG2 VAL K 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 2511 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 88 " -0.009 2.00e-02 2.50e+03 1.38e-02 3.81e+00 pdb=" CG TYR F 88 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR F 88 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR F 88 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR F 88 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 88 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 88 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 88 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.025 2.00e-02 2.50e+03 1.06e-02 3.07e+00 pdb=" N9 DA I -35 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.024 2.00e-02 2.50e+03 9.63e-03 2.78e+00 pdb=" N9 DG I 47 " 0.019 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.002 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 164 2.63 - 3.20: 12082 3.20 - 3.77: 25513 3.77 - 4.33: 32901 4.33 - 4.90: 48665 Nonbonded interactions: 119325 Sorted by model distance: nonbonded pdb=" OG SER L 22 " pdb=" OG1 THR L 36 " model vdw 2.063 3.040 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.106 2.496 nonbonded pdb=" NH2 ARG B 35 " pdb=" OP2 DG J 8 " model vdw 2.192 3.120 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.200 3.040 nonbonded pdb=" OG SER D 64 " pdb=" O GLY F 101 " model vdw 2.226 3.040 ... (remaining 119320 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 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 41.940 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 0.003 0.035 15462 Z= 0.197 Angle : 0.553 7.668 22156 Z= 0.322 Chirality : 0.035 0.160 2514 Planarity : 0.003 0.040 1792 Dihedral : 25.887 179.987 6570 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.88 (0.26), residues: 1056 helix: 2.33 (0.21), residues: 640 sheet: 1.42 (0.81), residues: 48 loop : -0.80 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 93 HIS 0.002 0.001 HIS D 82 PHE 0.010 0.001 PHE L 69 TYR 0.033 0.002 TYR F 88 ARG 0.014 0.000 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8580 (tppt) REVERT: D 83 TYR cc_start: 0.8301 (m-80) cc_final: 0.7966 (m-80) REVERT: D 116 LYS cc_start: 0.9178 (ttpp) cc_final: 0.8815 (tttt) REVERT: D 120 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8480 (tttp) REVERT: G 30 VAL cc_start: 0.9252 (t) cc_final: 0.9023 (m) REVERT: H 35 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8135 (mt-10) REVERT: K 41 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7631 (mm-40) REVERT: K 49 LEU cc_start: 0.8683 (tp) cc_final: 0.8430 (tp) REVERT: K 57 ARG cc_start: 0.7490 (mtp-110) cc_final: 0.6992 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3026 time to fit residues: 77.4074 Evaluate side-chains 150 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 0.0570 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15462 Z= 0.231 Angle : 0.586 11.512 22156 Z= 0.335 Chirality : 0.036 0.183 2514 Planarity : 0.004 0.035 1792 Dihedral : 28.896 179.477 4410 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.65 % Allowed : 9.99 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.88 (0.26), residues: 1056 helix: 2.39 (0.20), residues: 644 sheet: 1.22 (0.80), residues: 48 loop : -0.91 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 141 HIS 0.003 0.001 HIS L 32 PHE 0.008 0.001 PHE H 70 TYR 0.028 0.002 TYR H 83 ARG 0.008 0.000 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9166 (mmtt) cc_final: 0.8812 (tptt) REVERT: D 51 ASP cc_start: 0.8084 (t0) cc_final: 0.7797 (t0) REVERT: D 83 TYR cc_start: 0.8550 (m-80) cc_final: 0.7838 (m-10) REVERT: D 116 LYS cc_start: 0.9196 (ttpp) cc_final: 0.8807 (tttt) REVERT: D 120 LYS cc_start: 0.9026 (ttpt) cc_final: 0.8440 (tttp) REVERT: K 49 LEU cc_start: 0.8652 (tp) cc_final: 0.8434 (tp) REVERT: L 97 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8425 (tp) outliers start: 6 outliers final: 4 residues processed: 160 average time/residue: 0.2936 time to fit residues: 66.7141 Evaluate side-chains 159 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 15462 Z= 0.564 Angle : 0.742 10.049 22156 Z= 0.417 Chirality : 0.044 0.192 2514 Planarity : 0.005 0.036 1792 Dihedral : 29.177 178.558 4410 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.28 % Allowed : 13.68 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.09 (0.26), residues: 1056 helix: 1.79 (0.20), residues: 644 sheet: 0.74 (0.81), residues: 48 loop : -1.28 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 141 HIS 0.006 0.001 HIS D 82 PHE 0.014 0.002 PHE H 70 TYR 0.031 0.003 TYR H 83 ARG 0.009 0.001 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: A 37 LYS cc_start: 0.8922 (tptp) cc_final: 0.8710 (tptp) REVERT: C 73 ASN cc_start: 0.8549 (t0) cc_final: 0.8301 (t0) REVERT: D 46 LYS cc_start: 0.9214 (mmtt) cc_final: 0.8972 (mptt) REVERT: D 51 ASP cc_start: 0.8116 (t0) cc_final: 0.7893 (t0) REVERT: D 116 LYS cc_start: 0.9262 (ttpp) cc_final: 0.8925 (tttt) REVERT: D 120 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8579 (tttt) REVERT: H 51 ASP cc_start: 0.8849 (p0) cc_final: 0.8643 (p0) outliers start: 21 outliers final: 10 residues processed: 158 average time/residue: 0.3027 time to fit residues: 68.4584 Evaluate side-chains 151 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15462 Z= 0.235 Angle : 0.603 11.635 22156 Z= 0.342 Chirality : 0.036 0.212 2514 Planarity : 0.004 0.033 1792 Dihedral : 28.987 179.816 4410 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.98 % Allowed : 14.88 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.56 (0.26), residues: 1056 helix: 2.20 (0.21), residues: 646 sheet: 0.64 (0.78), residues: 48 loop : -1.14 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 141 HIS 0.003 0.001 HIS B 75 PHE 0.015 0.001 PHE L 62 TYR 0.030 0.002 TYR H 83 ARG 0.008 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9155 (mmtt) cc_final: 0.8837 (mptt) REVERT: D 83 TYR cc_start: 0.8745 (m-10) cc_final: 0.8251 (m-10) REVERT: D 116 LYS cc_start: 0.9199 (ttpp) cc_final: 0.8833 (tttt) REVERT: D 120 LYS cc_start: 0.8971 (ttpt) cc_final: 0.8554 (tttt) REVERT: L 147 MET cc_start: 0.4705 (OUTLIER) cc_final: 0.1948 (pmm) outliers start: 9 outliers final: 7 residues processed: 157 average time/residue: 0.3095 time to fit residues: 68.7814 Evaluate side-chains 156 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 147 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 0.0470 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 0.0070 chunk 31 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15462 Z= 0.176 Angle : 0.585 14.652 22156 Z= 0.328 Chirality : 0.035 0.218 2514 Planarity : 0.004 0.037 1792 Dihedral : 28.845 179.220 4410 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.09 % Allowed : 15.96 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.71 (0.26), residues: 1056 helix: 2.31 (0.21), residues: 650 sheet: 0.23 (0.76), residues: 48 loop : -1.01 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 61 HIS 0.003 0.001 HIS K 65 PHE 0.014 0.001 PHE L 62 TYR 0.028 0.001 TYR H 83 ARG 0.008 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8926 (mmtm) REVERT: D 51 ASP cc_start: 0.7932 (t0) cc_final: 0.7685 (t0) REVERT: D 71 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7710 (tm-30) REVERT: D 83 TYR cc_start: 0.8578 (m-10) cc_final: 0.8369 (m-10) REVERT: D 116 LYS cc_start: 0.9177 (ttpp) cc_final: 0.8820 (tttt) REVERT: D 120 LYS cc_start: 0.8944 (ttpt) cc_final: 0.8505 (tttt) REVERT: L 147 MET cc_start: 0.4603 (OUTLIER) cc_final: 0.2634 (pmm) outliers start: 10 outliers final: 9 residues processed: 164 average time/residue: 0.2978 time to fit residues: 68.4959 Evaluate side-chains 159 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain M residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 2.9990 chunk 112 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15462 Z= 0.187 Angle : 0.583 15.359 22156 Z= 0.327 Chirality : 0.035 0.216 2514 Planarity : 0.003 0.033 1792 Dihedral : 28.851 179.618 4410 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.63 % Allowed : 16.18 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.76 (0.26), residues: 1056 helix: 2.35 (0.20), residues: 651 sheet: 0.10 (0.76), residues: 48 loop : -0.98 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 61 HIS 0.003 0.001 HIS F 75 PHE 0.013 0.001 PHE L 62 TYR 0.020 0.001 TYR H 83 ARG 0.006 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7846 (mt-10) REVERT: D 46 LYS cc_start: 0.9164 (mmtt) cc_final: 0.8877 (mmtm) REVERT: D 51 ASP cc_start: 0.8073 (t0) cc_final: 0.7761 (t0) REVERT: D 59 MET cc_start: 0.8874 (tpp) cc_final: 0.8638 (tpt) REVERT: D 71 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7719 (tm-30) REVERT: D 83 TYR cc_start: 0.8555 (m-10) cc_final: 0.8323 (m-10) REVERT: D 116 LYS cc_start: 0.9181 (ttpp) cc_final: 0.8816 (tttt) REVERT: D 120 LYS cc_start: 0.8972 (ttpt) cc_final: 0.8475 (tttt) REVERT: E 59 GLU cc_start: 0.8780 (pm20) cc_final: 0.8360 (pm20) REVERT: H 33 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7570 (mtp-110) REVERT: K 49 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8168 (tp) REVERT: L 147 MET cc_start: 0.4662 (OUTLIER) cc_final: 0.2670 (pmm) outliers start: 15 outliers final: 9 residues processed: 162 average time/residue: 0.3112 time to fit residues: 71.4504 Evaluate side-chains 161 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 147 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15462 Z= 0.196 Angle : 0.587 12.059 22156 Z= 0.328 Chirality : 0.035 0.203 2514 Planarity : 0.004 0.033 1792 Dihedral : 28.842 179.221 4410 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.74 % Allowed : 16.61 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.77 (0.26), residues: 1056 helix: 2.31 (0.20), residues: 657 sheet: 0.16 (0.79), residues: 48 loop : -0.95 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 61 HIS 0.003 0.001 HIS F 75 PHE 0.012 0.001 PHE L 62 TYR 0.020 0.001 TYR D 40 ARG 0.006 0.000 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.371 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7949 (mt-10) REVERT: D 46 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8906 (mptt) REVERT: D 51 ASP cc_start: 0.8075 (t0) cc_final: 0.7758 (t0) REVERT: D 59 MET cc_start: 0.8858 (tpp) cc_final: 0.8618 (tpt) REVERT: D 71 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7715 (tm-30) REVERT: D 83 TYR cc_start: 0.8562 (m-10) cc_final: 0.8324 (m-10) REVERT: D 116 LYS cc_start: 0.9173 (ttpp) cc_final: 0.8807 (tttt) REVERT: D 120 LYS cc_start: 0.8949 (ttpt) cc_final: 0.8465 (tttt) REVERT: E 59 GLU cc_start: 0.8773 (pm20) cc_final: 0.8374 (pm20) REVERT: E 61 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8891 (mm) REVERT: H 33 ARG cc_start: 0.7871 (mtp85) cc_final: 0.7548 (mtp-110) REVERT: H 121 TYR cc_start: 0.9167 (t80) cc_final: 0.8939 (t80) REVERT: K 49 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8144 (tp) REVERT: L 147 MET cc_start: 0.4696 (OUTLIER) cc_final: 0.2659 (pmm) outliers start: 16 outliers final: 11 residues processed: 158 average time/residue: 0.3185 time to fit residues: 71.2419 Evaluate side-chains 164 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 147 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 0.3980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15462 Z= 0.192 Angle : 0.588 13.964 22156 Z= 0.327 Chirality : 0.035 0.186 2514 Planarity : 0.004 0.036 1792 Dihedral : 28.832 179.123 4410 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.63 % Allowed : 16.83 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.78 (0.26), residues: 1056 helix: 2.33 (0.20), residues: 657 sheet: 0.10 (0.80), residues: 48 loop : -0.95 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 61 HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE L 62 TYR 0.019 0.001 TYR H 83 ARG 0.009 0.000 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7952 (mt-10) REVERT: D 46 LYS cc_start: 0.9145 (mmtt) cc_final: 0.8916 (mptt) REVERT: D 51 ASP cc_start: 0.8088 (t0) cc_final: 0.7773 (t0) REVERT: D 59 MET cc_start: 0.8829 (tpp) cc_final: 0.8570 (tpt) REVERT: D 71 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7705 (tm-30) REVERT: D 83 TYR cc_start: 0.8557 (m-10) cc_final: 0.8331 (m-10) REVERT: D 116 LYS cc_start: 0.9169 (ttpp) cc_final: 0.8801 (tttt) REVERT: D 120 LYS cc_start: 0.8917 (ttpt) cc_final: 0.8443 (tttt) REVERT: E 61 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8889 (mm) REVERT: H 33 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7573 (mtp-110) REVERT: H 121 TYR cc_start: 0.9153 (t80) cc_final: 0.8911 (t80) REVERT: K 49 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8141 (tp) REVERT: L 147 MET cc_start: 0.4705 (OUTLIER) cc_final: 0.2681 (pmm) outliers start: 15 outliers final: 11 residues processed: 157 average time/residue: 0.3133 time to fit residues: 70.4362 Evaluate side-chains 164 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 147 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 119 optimal weight: 0.0670 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15462 Z= 0.179 Angle : 0.584 13.507 22156 Z= 0.325 Chirality : 0.035 0.200 2514 Planarity : 0.004 0.034 1792 Dihedral : 28.799 178.956 4410 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.74 % Allowed : 16.83 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.81 (0.26), residues: 1056 helix: 2.35 (0.20), residues: 663 sheet: 0.05 (0.80), residues: 48 loop : -0.97 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 61 HIS 0.005 0.001 HIS M 68 PHE 0.010 0.001 PHE L 62 TYR 0.022 0.001 TYR D 40 ARG 0.007 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9166 (mmtt) cc_final: 0.8925 (mptt) REVERT: D 51 ASP cc_start: 0.8061 (t0) cc_final: 0.7750 (t0) REVERT: D 59 MET cc_start: 0.8778 (tpp) cc_final: 0.8533 (tpt) REVERT: D 71 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7738 (tm-30) REVERT: D 83 TYR cc_start: 0.8575 (m-10) cc_final: 0.8302 (m-10) REVERT: D 116 LYS cc_start: 0.9187 (ttpp) cc_final: 0.8843 (tttt) REVERT: D 120 LYS cc_start: 0.8909 (ttpt) cc_final: 0.8419 (tttt) REVERT: E 61 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8903 (mm) REVERT: H 33 ARG cc_start: 0.7906 (mtp85) cc_final: 0.7568 (mtp-110) REVERT: H 121 TYR cc_start: 0.9147 (t80) cc_final: 0.8932 (t80) REVERT: L 10 LEU cc_start: 0.8367 (pp) cc_final: 0.8134 (pt) REVERT: L 147 MET cc_start: 0.4780 (OUTLIER) cc_final: 0.2715 (pmm) outliers start: 16 outliers final: 13 residues processed: 162 average time/residue: 0.3059 time to fit residues: 70.5321 Evaluate side-chains 166 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 147 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15462 Z= 0.291 Angle : 0.632 12.939 22156 Z= 0.348 Chirality : 0.037 0.231 2514 Planarity : 0.004 0.032 1792 Dihedral : 28.915 178.360 4410 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.63 % Allowed : 16.94 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.63 (0.26), residues: 1056 helix: 2.23 (0.20), residues: 662 sheet: -0.01 (0.79), residues: 48 loop : -1.10 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 61 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE H 70 TYR 0.022 0.002 TYR H 83 ARG 0.006 0.000 ARG C 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7987 (mm-30) REVERT: D 46 LYS cc_start: 0.9198 (mmtt) cc_final: 0.8993 (mptt) REVERT: D 51 ASP cc_start: 0.8051 (t0) cc_final: 0.7781 (t0) REVERT: D 83 TYR cc_start: 0.8674 (m-10) cc_final: 0.8375 (m-10) REVERT: D 116 LYS cc_start: 0.9188 (ttpp) cc_final: 0.8839 (tttt) REVERT: D 120 LYS cc_start: 0.8955 (ttpt) cc_final: 0.8452 (tttt) REVERT: E 61 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8851 (mm) REVERT: H 33 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7604 (mtp-110) REVERT: H 121 TYR cc_start: 0.9177 (t80) cc_final: 0.8932 (t80) REVERT: L 147 MET cc_start: 0.4911 (OUTLIER) cc_final: 0.2769 (pmm) outliers start: 15 outliers final: 11 residues processed: 155 average time/residue: 0.3204 time to fit residues: 70.6055 Evaluate side-chains 159 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 147 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.143191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105428 restraints weight = 30329.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110674 restraints weight = 62972.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109000 restraints weight = 28748.043| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15462 Z= 0.188 Angle : 0.597 12.991 22156 Z= 0.330 Chirality : 0.035 0.198 2514 Planarity : 0.003 0.034 1792 Dihedral : 28.842 179.085 4410 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.30 % Allowed : 17.92 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.78 (0.26), residues: 1056 helix: 2.33 (0.20), residues: 662 sheet: 0.08 (0.79), residues: 48 loop : -1.01 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 61 HIS 0.002 0.001 HIS B 75 PHE 0.009 0.001 PHE L 62 TYR 0.024 0.001 TYR L 60 ARG 0.006 0.000 ARG C 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2323.58 seconds wall clock time: 43 minutes 56.09 seconds (2636.09 seconds total)