Starting phenix.real_space_refine on Sat Oct 11 11:27:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sn9_40617/10_2025/8sn9_40617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sn9_40617/10_2025/8sn9_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_40617/10_2025/8sn9_40617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sn9_40617/10_2025/8sn9_40617.map" model { file = "/net/cci-nas-00/data/ceres_data/8sn9_40617/10_2025/8sn9_40617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sn9_40617/10_2025/8sn9_40617.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.03, per 1000 atoms: 0.21 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: 1.01 Conformation dependent library (CDL) restraints added in 406.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.05 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: 2.35 Time building geometry restraints manager: 1.30 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: 1.420 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.910 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.170 ------------------------------------------------------------------------------- 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 15472 Z= 0.159 Angle : 0.557 7.668 22171 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.000 ARG L 15 TYR 0.033 0.002 TYR F 88 PHE 0.010 0.001 PHE L 69 TRP 0.017 0.002 TRP L 93 HIS 0.002 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00349 (15462) covalent geometry : angle 0.55309 (22156) hydrogen bonds : bond 0.10647 ( 841) hydrogen bonds : angle 3.84937 ( 2147) metal coordination : bond 0.00697 ( 8) metal coordination : angle 3.45337 ( 9) link_TRANS : bond 0.00058 ( 2) link_TRANS : angle 0.24804 ( 6) *********************** 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 : 0.340 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: 0.1359 time to fit residues: 35.0071 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 : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110299 restraints weight = 37605.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.111956 restraints weight = 85312.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113635 restraints weight = 29096.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114651 restraints weight = 18482.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.114986 restraints weight = 13037.532| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15472 Z= 0.212 Angle : 0.614 11.043 22171 Z= 0.346 Chirality : 0.037 0.194 2514 Planarity : 0.004 0.035 1792 Dihedral : 28.932 179.350 4410 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.76 % Allowed : 10.53 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.26), residues: 1056 helix: 2.31 (0.20), residues: 644 sheet: 1.15 (0.80), residues: 48 loop : -0.96 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 33 TYR 0.028 0.002 TYR H 83 PHE 0.009 0.001 PHE H 70 TRP 0.008 0.001 TRP L 141 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00489 (15462) covalent geometry : angle 0.60756 (22156) hydrogen bonds : bond 0.05292 ( 841) hydrogen bonds : angle 3.38669 ( 2147) metal coordination : bond 0.00967 ( 8) metal coordination : angle 4.49697 ( 9) link_TRANS : bond 0.00302 ( 2) link_TRANS : angle 0.38207 ( 6) *********************** 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 162 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: D 46 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8553 (tptt) REVERT: D 51 ASP cc_start: 0.7754 (t0) cc_final: 0.7547 (t0) REVERT: D 83 TYR cc_start: 0.8593 (m-80) cc_final: 0.7613 (m-10) REVERT: D 116 LYS cc_start: 0.9065 (ttpp) cc_final: 0.8718 (tttt) REVERT: D 120 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8430 (tttt) REVERT: L 97 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8218 (tp) outliers start: 7 outliers final: 4 residues processed: 157 average time/residue: 0.1369 time to fit residues: 30.5103 Evaluate side-chains 153 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 73 GLU 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 8 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 100 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 L 34 GLN M 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.142662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111583 restraints weight = 38081.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113445 restraints weight = 83970.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114991 restraints weight = 28907.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.115837 restraints weight = 19212.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116805 restraints weight = 13678.020| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15472 Z= 0.160 Angle : 0.576 11.604 22171 Z= 0.326 Chirality : 0.035 0.212 2514 Planarity : 0.004 0.035 1792 Dihedral : 28.800 179.733 4410 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.52 % Allowed : 12.38 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.26), residues: 1056 helix: 2.39 (0.21), residues: 646 sheet: 0.93 (0.79), residues: 48 loop : -0.91 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 42 TYR 0.024 0.002 TYR H 83 PHE 0.009 0.001 PHE D 65 TRP 0.009 0.001 TRP L 141 HIS 0.005 0.001 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00357 (15462) covalent geometry : angle 0.57100 (22156) hydrogen bonds : bond 0.04578 ( 841) hydrogen bonds : angle 3.15108 ( 2147) metal coordination : bond 0.00618 ( 8) metal coordination : angle 3.67763 ( 9) link_TRANS : bond 0.00131 ( 2) link_TRANS : angle 0.30869 ( 6) *********************** 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 169 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: D 46 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8536 (tptt) REVERT: D 51 ASP cc_start: 0.7729 (t0) cc_final: 0.7446 (t0) REVERT: D 71 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7731 (tm-30) REVERT: D 83 TYR cc_start: 0.8573 (m-10) cc_final: 0.7894 (m-10) REVERT: D 116 LYS cc_start: 0.9065 (ttpp) cc_final: 0.8720 (tttt) REVERT: D 120 LYS cc_start: 0.8835 (ttpt) cc_final: 0.8415 (tttt) REVERT: H 51 ASP cc_start: 0.8224 (p0) cc_final: 0.8013 (p0) REVERT: H 121 TYR cc_start: 0.8991 (t80) cc_final: 0.8681 (t80) outliers start: 14 outliers final: 5 residues processed: 157 average time/residue: 0.1480 time to fit residues: 32.5022 Evaluate side-chains 153 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 96 THR Chi-restraints excluded: chain L residue 30 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 125 optimal weight: 30.0000 chunk 70 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.142367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.094496 restraints weight = 42534.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.090157 restraints weight = 36181.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.088695 restraints weight = 31376.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.089305 restraints weight = 26074.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.089409 restraints weight = 23118.116| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15472 Z= 0.170 Angle : 0.584 11.856 22171 Z= 0.329 Chirality : 0.036 0.213 2514 Planarity : 0.004 0.034 1792 Dihedral : 28.821 179.398 4410 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.52 % Allowed : 14.22 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.26), residues: 1056 helix: 2.39 (0.21), residues: 647 sheet: 0.77 (0.80), residues: 48 loop : -0.88 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 33 TYR 0.018 0.001 TYR H 83 PHE 0.017 0.001 PHE L 62 TRP 0.009 0.001 TRP L 141 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00383 (15462) covalent geometry : angle 0.58026 (22156) hydrogen bonds : bond 0.04653 ( 841) hydrogen bonds : angle 3.15417 ( 2147) metal coordination : bond 0.00583 ( 8) metal coordination : angle 3.22847 ( 9) link_TRANS : bond 0.00154 ( 2) link_TRANS : angle 0.28317 ( 6) *********************** 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 172 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8647 (tptt) REVERT: D 51 ASP cc_start: 0.8033 (t0) cc_final: 0.7796 (t0) REVERT: D 71 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7786 (tm-30) REVERT: D 83 TYR cc_start: 0.8609 (m-10) cc_final: 0.7925 (m-80) REVERT: D 116 LYS cc_start: 0.9147 (ttpp) cc_final: 0.8774 (tttt) REVERT: D 120 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8554 (tttt) REVERT: H 121 TYR cc_start: 0.9122 (t80) cc_final: 0.8869 (t80) REVERT: L 32 HIS cc_start: 0.7558 (m-70) cc_final: 0.7308 (m-70) outliers start: 14 outliers final: 11 residues processed: 162 average time/residue: 0.1404 time to fit residues: 32.2705 Evaluate side-chains 163 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 112 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 0.0980 chunk 104 optimal weight: 0.1980 chunk 90 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 119 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** L 34 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 = 0.3834 r_free = 0.3834 target = 0.143910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.096807 restraints weight = 50272.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.091075 restraints weight = 41191.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.092176 restraints weight = 37624.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.092778 restraints weight = 26273.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.092631 restraints weight = 23039.924| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15472 Z= 0.145 Angle : 0.570 12.116 22171 Z= 0.320 Chirality : 0.035 0.194 2514 Planarity : 0.003 0.035 1792 Dihedral : 28.758 179.446 4410 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.30 % Allowed : 15.42 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.26), residues: 1056 helix: 2.45 (0.20), residues: 650 sheet: 0.67 (0.80), residues: 48 loop : -0.86 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.025 0.001 TYR H 83 PHE 0.016 0.001 PHE L 62 TRP 0.009 0.001 TRP K 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00313 (15462) covalent geometry : angle 0.56538 (22156) hydrogen bonds : bond 0.04289 ( 841) hydrogen bonds : angle 3.01553 ( 2147) metal coordination : bond 0.00603 ( 8) metal coordination : angle 3.70640 ( 9) link_TRANS : bond 0.00119 ( 2) link_TRANS : angle 0.60834 ( 6) *********************** 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: 12 poor density : 159 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9035 (mmtt) cc_final: 0.8673 (tptt) REVERT: D 71 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7720 (tm-30) REVERT: D 83 TYR cc_start: 0.8637 (m-10) cc_final: 0.8028 (m-10) REVERT: D 116 LYS cc_start: 0.9098 (ttpp) cc_final: 0.8706 (tttt) REVERT: D 120 LYS cc_start: 0.8924 (ttpt) cc_final: 0.8461 (tttt) REVERT: E 59 GLU cc_start: 0.8706 (pm20) cc_final: 0.8402 (pm20) REVERT: H 33 ARG cc_start: 0.8350 (mtp85) cc_final: 0.7536 (mtp-110) REVERT: H 121 TYR cc_start: 0.9090 (t80) cc_final: 0.8823 (t80) outliers start: 12 outliers final: 9 residues processed: 163 average time/residue: 0.1439 time to fit residues: 33.1676 Evaluate side-chains 160 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 61 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 110 optimal weight: 40.0000 chunk 128 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 112 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.142210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.093542 restraints weight = 49856.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090864 restraints weight = 40693.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.089572 restraints weight = 29860.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.089498 restraints weight = 23299.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.089768 restraints weight = 23768.357| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15472 Z= 0.177 Angle : 0.592 12.866 22171 Z= 0.331 Chirality : 0.036 0.201 2514 Planarity : 0.004 0.033 1792 Dihedral : 28.824 178.821 4410 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.52 % Allowed : 15.64 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.26), residues: 1056 helix: 2.39 (0.20), residues: 650 sheet: 0.66 (0.83), residues: 48 loop : -0.92 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 99 TYR 0.021 0.001 TYR H 83 PHE 0.014 0.001 PHE L 62 TRP 0.019 0.002 TRP K 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00401 (15462) covalent geometry : angle 0.58850 (22156) hydrogen bonds : bond 0.04746 ( 841) hydrogen bonds : angle 3.14967 ( 2147) metal coordination : bond 0.00610 ( 8) metal coordination : angle 3.41479 ( 9) link_TRANS : bond 0.00116 ( 2) link_TRANS : angle 0.50230 ( 6) *********************** 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 169 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8810 (mptt) REVERT: D 71 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7779 (tm-30) REVERT: D 83 TYR cc_start: 0.8660 (m-10) cc_final: 0.8330 (m-80) REVERT: D 116 LYS cc_start: 0.9142 (ttpp) cc_final: 0.8755 (tttt) REVERT: D 120 LYS cc_start: 0.8957 (ttpt) cc_final: 0.8510 (tttt) REVERT: E 59 GLU cc_start: 0.8759 (pm20) cc_final: 0.8488 (pm20) REVERT: H 33 ARG cc_start: 0.8434 (mtp85) cc_final: 0.7617 (mtp-110) outliers start: 14 outliers final: 11 residues processed: 161 average time/residue: 0.1366 time to fit residues: 31.2533 Evaluate side-chains 162 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.0000 chunk 104 optimal weight: 0.4980 chunk 128 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.144116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.097361 restraints weight = 42753.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.092551 restraints weight = 39283.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.092268 restraints weight = 33230.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.092275 restraints weight = 26017.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.092339 restraints weight = 22920.608| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15472 Z= 0.144 Angle : 0.573 12.352 22171 Z= 0.321 Chirality : 0.034 0.203 2514 Planarity : 0.004 0.035 1792 Dihedral : 28.757 179.352 4410 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.09 % Allowed : 16.50 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.26), residues: 1056 helix: 2.40 (0.20), residues: 662 sheet: 0.54 (0.81), residues: 48 loop : -0.84 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 99 TYR 0.021 0.001 TYR H 83 PHE 0.008 0.001 PHE D 65 TRP 0.019 0.002 TRP K 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00308 (15462) covalent geometry : angle 0.56995 (22156) hydrogen bonds : bond 0.04282 ( 841) hydrogen bonds : angle 2.98335 ( 2147) metal coordination : bond 0.00522 ( 8) metal coordination : angle 3.09242 ( 9) link_TRANS : bond 0.00086 ( 2) link_TRANS : angle 0.58087 ( 6) *********************** 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 162 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.423 Fit side-chains REVERT: D 46 LYS cc_start: 0.9068 (mmtt) cc_final: 0.8792 (mptt) REVERT: D 51 ASP cc_start: 0.7541 (t0) cc_final: 0.7309 (t0) REVERT: D 83 TYR cc_start: 0.8557 (m-10) cc_final: 0.7985 (m-10) REVERT: D 116 LYS cc_start: 0.9088 (ttpp) cc_final: 0.8702 (tttt) REVERT: D 120 LYS cc_start: 0.8906 (ttpt) cc_final: 0.8480 (tttt) REVERT: H 33 ARG cc_start: 0.8416 (mtp85) cc_final: 0.7604 (mtp-110) REVERT: H 42 TYR cc_start: 0.8136 (t80) cc_final: 0.7173 (t80) outliers start: 10 outliers final: 8 residues processed: 157 average time/residue: 0.1430 time to fit residues: 32.0285 Evaluate side-chains 154 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 VAL 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 H residue 119 THR Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 37 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 75 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 121 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 L 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101778 restraints weight = 29614.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107223 restraints weight = 62046.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105608 restraints weight = 27563.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.106295 restraints weight = 22774.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106599 restraints weight = 19050.511| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15472 Z= 0.217 Angle : 0.628 13.701 22171 Z= 0.347 Chirality : 0.037 0.219 2514 Planarity : 0.004 0.033 1792 Dihedral : 28.931 178.600 4410 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.41 % Allowed : 16.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.26), residues: 1056 helix: 2.26 (0.20), residues: 661 sheet: 0.22 (0.78), residues: 48 loop : -0.99 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 57 TYR 0.022 0.002 TYR H 83 PHE 0.012 0.001 PHE L 51 TRP 0.017 0.002 TRP K 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00503 (15462) covalent geometry : angle 0.62450 (22156) hydrogen bonds : bond 0.05276 ( 841) hydrogen bonds : angle 3.30893 ( 2147) metal coordination : bond 0.00685 ( 8) metal coordination : angle 3.23842 ( 9) link_TRANS : bond 0.00193 ( 2) link_TRANS : angle 0.45535 ( 6) *********************** 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 163 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9110 (mmtt) cc_final: 0.8885 (mptt) REVERT: D 51 ASP cc_start: 0.7892 (t0) cc_final: 0.7652 (t0) REVERT: D 83 TYR cc_start: 0.8701 (m-10) cc_final: 0.8038 (m-10) REVERT: D 120 LYS cc_start: 0.8970 (ttpt) cc_final: 0.8576 (tttt) REVERT: E 59 GLU cc_start: 0.8715 (pm20) cc_final: 0.8223 (pm20) REVERT: H 33 ARG cc_start: 0.8259 (mtp85) cc_final: 0.7776 (mtp-110) REVERT: H 121 TYR cc_start: 0.9150 (t80) cc_final: 0.8915 (t80) outliers start: 13 outliers final: 8 residues processed: 158 average time/residue: 0.1538 time to fit residues: 34.0744 Evaluate side-chains 152 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 119 THR 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 L residue 37 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 56 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 chunk 54 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 102 optimal weight: 0.0270 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.143606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109217 restraints weight = 35815.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.112757 restraints weight = 80564.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113165 restraints weight = 29216.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114735 restraints weight = 21884.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115027 restraints weight = 15834.869| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15472 Z= 0.145 Angle : 0.589 13.232 22171 Z= 0.326 Chirality : 0.035 0.255 2514 Planarity : 0.003 0.036 1792 Dihedral : 28.802 179.332 4410 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.76 % Allowed : 17.16 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.26), residues: 1056 helix: 2.39 (0.20), residues: 662 sheet: 0.20 (0.78), residues: 48 loop : -0.92 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 99 TYR 0.023 0.001 TYR H 83 PHE 0.009 0.001 PHE D 65 TRP 0.020 0.002 TRP K 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00314 (15462) covalent geometry : angle 0.58453 (22156) hydrogen bonds : bond 0.04299 ( 841) hydrogen bonds : angle 3.00702 ( 2147) metal coordination : bond 0.00588 ( 8) metal coordination : angle 3.64959 ( 9) link_TRANS : bond 0.00078 ( 2) link_TRANS : angle 0.60379 ( 6) *********************** 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 160 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9072 (mmtt) cc_final: 0.8779 (mptt) REVERT: D 51 ASP cc_start: 0.7793 (t0) cc_final: 0.7576 (t0) REVERT: D 83 TYR cc_start: 0.8618 (m-10) cc_final: 0.8097 (m-10) REVERT: D 120 LYS cc_start: 0.8923 (ttpt) cc_final: 0.8445 (tttt) REVERT: E 59 GLU cc_start: 0.8664 (pm20) cc_final: 0.8132 (pm20) REVERT: H 33 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7774 (mtp-110) REVERT: H 35 GLU cc_start: 0.8153 (tt0) cc_final: 0.7808 (mt-10) REVERT: H 121 TYR cc_start: 0.9053 (t80) cc_final: 0.8796 (t80) outliers start: 7 outliers final: 6 residues processed: 157 average time/residue: 0.1413 time to fit residues: 31.5404 Evaluate side-chains 158 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 37 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 19 optimal weight: 0.0060 chunk 42 optimal weight: 1.9990 chunk 121 optimal weight: 30.0000 chunk 83 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.142641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110621 restraints weight = 37727.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112478 restraints weight = 84984.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113995 restraints weight = 30864.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114752 restraints weight = 20849.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116385 restraints weight = 14954.141| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15472 Z= 0.166 Angle : 0.603 18.344 22171 Z= 0.331 Chirality : 0.035 0.230 2514 Planarity : 0.003 0.033 1792 Dihedral : 28.838 178.839 4410 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.76 % Allowed : 17.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.26), residues: 1056 helix: 2.35 (0.20), residues: 662 sheet: 0.16 (0.78), residues: 48 loop : -0.92 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 99 TYR 0.027 0.002 TYR L 60 PHE 0.014 0.001 PHE L 51 TRP 0.019 0.002 TRP K 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00373 (15462) covalent geometry : angle 0.59899 (22156) hydrogen bonds : bond 0.04523 ( 841) hydrogen bonds : angle 3.11372 ( 2147) metal coordination : bond 0.00551 ( 8) metal coordination : angle 3.45567 ( 9) link_TRANS : bond 0.00065 ( 2) link_TRANS : angle 0.51665 ( 6) ********************** 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 158 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: D 46 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8781 (mptt) REVERT: D 83 TYR cc_start: 0.8652 (m-10) cc_final: 0.8159 (m-10) REVERT: D 120 LYS cc_start: 0.8865 (ttpt) cc_final: 0.8409 (tttt) REVERT: E 59 GLU cc_start: 0.8688 (pm20) cc_final: 0.8464 (pm20) REVERT: H 33 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7786 (mtp-110) REVERT: H 35 GLU cc_start: 0.8088 (tt0) cc_final: 0.7703 (mt-10) REVERT: H 121 TYR cc_start: 0.8999 (t80) cc_final: 0.8759 (t80) outliers start: 7 outliers final: 6 residues processed: 155 average time/residue: 0.1406 time to fit residues: 30.9460 Evaluate side-chains 156 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 37 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 128 optimal weight: 0.3980 chunk 125 optimal weight: 40.0000 chunk 108 optimal weight: 2.9990 chunk 93 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.143442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111582 restraints weight = 36935.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113647 restraints weight = 86064.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114744 restraints weight = 31473.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115534 restraints weight = 22267.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.117433 restraints weight = 15721.851| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15472 Z= 0.154 Angle : 0.605 17.352 22171 Z= 0.331 Chirality : 0.035 0.236 2514 Planarity : 0.004 0.034 1792 Dihedral : 28.817 178.907 4410 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.87 % Allowed : 17.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.26), residues: 1056 helix: 2.37 (0.20), residues: 662 sheet: 0.27 (0.78), residues: 48 loop : -0.87 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 57 TYR 0.030 0.002 TYR L 60 PHE 0.008 0.001 PHE D 65 TRP 0.021 0.002 TRP K 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00338 (15462) covalent geometry : angle 0.60162 (22156) hydrogen bonds : bond 0.04358 ( 841) hydrogen bonds : angle 3.05415 ( 2147) metal coordination : bond 0.00528 ( 8) metal coordination : angle 3.30589 ( 9) link_TRANS : bond 0.00062 ( 2) link_TRANS : angle 0.55371 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2286.99 seconds wall clock time: 40 minutes 8.93 seconds (2408.93 seconds total)