Starting phenix.real_space_refine on Sun Aug 9 08:01:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jsh_36620/08_2026/8jsh_36620.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsh_36620/08_2026/8jsh_36620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8jsh_36620/08_2026/8jsh_36620.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jsh_36620/08_2026/8jsh_36620.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jsh_36620/08_2026/8jsh_36620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsh_36620/08_2026/8jsh_36620.map" model { file = "/net/cci-nas-00/data/ceres_data/8jsh_36620/08_2026/8jsh_36620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsh_36620/08_2026/8jsh_36620.cif" } resolution = 4.4 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= 0.001 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: 5 Type Number sf(0) Gaussians P 1073 5.49 5 S 44 5.16 5 C 17320 2.51 5 N 6399 2.21 5 O 9495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34331 Number of models: 1 Model: "" Number of chains: 14 Chain: "1" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "2" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "3" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "P" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "g" Number of atoms: 23057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 23057 Classifications: {'RNAv2': 1074} Modifications used: {'rna2p_pur': 86, 'rna2p_pyr': 55, 'rna3p_pur': 531, 'rna3p_pyr': 402} Link IDs: {'rna2p': 140, 'rna3p': 933} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "k" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "l" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "n" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "p" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "q" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "t" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "u" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "y" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "A" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1342 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Time building chain proxies: 6.54, per 1000 atoms: 0.19 Number of scatterers: 34331 At special positions: 0 Unit cell: (212.4, 157.2, 178.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 1073 15.00 O 9495 8.00 N 6399 7.00 C 17320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 641.9 milliseconds 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2654 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 15 sheets defined 40.1% alpha, 16.5% beta 337 base pairs and 499 stacking pairs defined. Time for finding SS restraints: 4.78 Creating SS restraints... Processing helix chain '1' and resid 24 through 30 removed outlier: 3.776A pdb=" N ASN 1 30 " --> pdb=" O ALA 1 26 " (cutoff:3.500A) Processing helix chain '1' and resid 40 through 45 removed outlier: 3.690A pdb=" N THR 1 44 " --> pdb=" O PRO 1 40 " (cutoff:3.500A) Processing helix chain '1' and resid 47 through 64 Processing helix chain '2' and resid 16 through 24 Processing helix chain '2' and resid 24 through 33 removed outlier: 4.382A pdb=" N LEU 2 28 " --> pdb=" O LYS 2 24 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG 2 33 " --> pdb=" O ALA 2 29 " (cutoff:3.500A) Processing helix chain '2' and resid 39 through 44 removed outlier: 3.606A pdb=" N GLU 2 43 " --> pdb=" O LYS 2 39 " (cutoff:3.500A) Processing helix chain '2' and resid 46 through 51 Processing helix chain '3' and resid 5 through 41 removed outlier: 4.033A pdb=" N ARG 3 9 " --> pdb=" O SER 3 5 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 64 Proline residue: 3 55 - end of helix Processing helix chain '3' and resid 68 through 86 removed outlier: 3.560A pdb=" N LYS 3 84 " --> pdb=" O ALA 3 80 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 68 removed outlier: 4.114A pdb=" N ARG k 67 " --> pdb=" O MET k 63 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG k 68 " --> pdb=" O GLU k 64 " (cutoff:3.500A) Processing helix chain 'k' and resid 110 through 116 Processing helix chain 'k' and resid 131 through 136 Processing helix chain 'k' and resid 138 through 145 Processing helix chain 'k' and resid 148 through 155 removed outlier: 3.723A pdb=" N VAL k 152 " --> pdb=" O SER k 148 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 15 removed outlier: 4.403A pdb=" N LEU l 10 " --> pdb=" O PRO l 6 " (cutoff:3.500A) Processing helix chain 'l' and resid 48 through 65 removed outlier: 3.794A pdb=" N GLN l 53 " --> pdb=" O ASP l 49 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR l 64 " --> pdb=" O VAL l 60 " (cutoff:3.500A) Processing helix chain 'l' and resid 67 through 81 removed outlier: 3.513A pdb=" N PHE l 71 " --> pdb=" O LEU l 67 " (cutoff:3.500A) Processing helix chain 'l' and resid 84 through 95 Processing helix chain 'l' and resid 96 through 104 Processing helix chain 'l' and resid 109 through 119 Processing helix chain 'l' and resid 151 through 161 removed outlier: 3.757A pdb=" N ALA l 157 " --> pdb=" O ARG l 153 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU l 159 " --> pdb=" O LYS l 155 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU l 160 " --> pdb=" O ALA l 156 " (cutoff:3.500A) Processing helix chain 'l' and resid 186 through 190 Processing helix chain 'l' and resid 195 through 205 removed outlier: 3.949A pdb=" N ILE l 199 " --> pdb=" O ASN l 195 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS l 205 " --> pdb=" O GLU l 201 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 15 removed outlier: 3.807A pdb=" N SER n 15 " --> pdb=" O PRO n 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 12 through 15' Processing helix chain 'n' and resid 17 through 32 removed outlier: 3.707A pdb=" N ALA n 32 " --> pdb=" O ALA n 28 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 81 removed outlier: 4.265A pdb=" N ILE n 71 " --> pdb=" O PRO n 67 " (cutoff:3.500A) Processing helix chain 'p' and resid 4 through 20 Processing helix chain 'p' and resid 29 through 43 Processing helix chain 'p' and resid 94 through 98 Processing helix chain 'p' and resid 112 through 119 Processing helix chain 'q' and resid 47 through 50 Processing helix chain 'q' and resid 58 through 74 Processing helix chain 'q' and resid 93 through 101 Processing helix chain 't' and resid 2 through 9 Processing helix chain 'u' and resid 3 through 15 Processing helix chain 'u' and resid 19 through 22 removed outlier: 4.529A pdb=" N GLY u 22 " --> pdb=" O ASN u 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 19 through 22' Processing helix chain 'u' and resid 23 through 44 removed outlier: 3.689A pdb=" N GLN u 27 " --> pdb=" O SER u 23 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY u 40 " --> pdb=" O ASN u 36 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS u 41 " --> pdb=" O HIS u 37 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU u 44 " --> pdb=" O GLY u 40 " (cutoff:3.500A) Processing helix chain 'u' and resid 48 through 73 removed outlier: 3.708A pdb=" N ARG u 52 " --> pdb=" O ASP u 48 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY u 54 " --> pdb=" O HIS u 50 " (cutoff:3.500A) Processing helix chain 'u' and resid 73 through 85 Processing helix chain 'y' and resid 54 through 64 Processing helix chain 'y' and resid 68 through 79 Processing helix chain 'A' and resid 15 through 19 removed outlier: 3.524A pdb=" N ILE A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 49 removed outlier: 3.884A pdb=" N ALA A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 87 Processing helix chain 'A' and resid 105 through 120 Processing helix chain 'A' and resid 137 through 152 removed outlier: 3.931A pdb=" N GLY A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 7 through 10 removed outlier: 5.824A pdb=" N SER P 71 " --> pdb=" O CYS P 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 7 through 10 removed outlier: 3.650A pdb=" N VAL P 57 " --> pdb=" O VAL P 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 20 through 29 removed outlier: 3.614A pdb=" N ARG P 26 " --> pdb=" O ARG P 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'k' and resid 11 through 21 removed outlier: 7.146A pdb=" N LEU k 35 " --> pdb=" O ILE k 15 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL k 17 " --> pdb=" O THR k 33 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR k 33 " --> pdb=" O VAL k 17 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG k 19 " --> pdb=" O SER k 31 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER k 31 " --> pdb=" O ARG k 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'k' and resid 11 through 21 removed outlier: 7.146A pdb=" N LEU k 35 " --> pdb=" O ILE k 15 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL k 17 " --> pdb=" O THR k 33 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR k 33 " --> pdb=" O VAL k 17 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG k 19 " --> pdb=" O SER k 31 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER k 31 " --> pdb=" O ARG k 19 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'k' and resid 84 through 88 removed outlier: 4.028A pdb=" N VAL k 84 " --> pdb=" O MET k 95 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET k 95 " --> pdb=" O VAL k 84 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY k 86 " --> pdb=" O VAL k 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'l' and resid 127 through 128 Processing sheet with id=AA8, first strand: chain 'n' and resid 35 through 45 removed outlier: 7.103A pdb=" N HIS n 37 " --> pdb=" O GLU n 65 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N GLU n 65 " --> pdb=" O HIS n 37 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU n 39 " --> pdb=" O ASN n 63 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASN n 63 " --> pdb=" O LEU n 39 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP n 41 " --> pdb=" O LEU n 61 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU n 61 " --> pdb=" O ASP n 41 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY n 43 " --> pdb=" O TYR n 59 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA n 57 " --> pdb=" O ARG n 45 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU n 5 " --> pdb=" O MET n 90 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET n 9 " --> pdb=" O ARG n 86 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG n 86 " --> pdb=" O MET n 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'p' and resid 23 through 27 removed outlier: 3.810A pdb=" N VAL p 24 " --> pdb=" O LEU p 60 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'p' and resid 108 through 111 removed outlier: 3.697A pdb=" N VAL p 103 " --> pdb=" O MET p 110 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE p 100 " --> pdb=" O TYR p 127 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TYR p 127 " --> pdb=" O ILE p 100 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL p 102 " --> pdb=" O ILE p 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'q' and resid 42 through 45 removed outlier: 3.513A pdb=" N VAL q 31 " --> pdb=" O ALA q 44 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA q 20 " --> pdb=" O MET q 84 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS q 86 " --> pdb=" O ALA q 20 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE q 22 " --> pdb=" O LYS q 86 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU q 81 " --> pdb=" O THR q 107 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE q 109 " --> pdb=" O LEU q 81 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL q 83 " --> pdb=" O ILE q 109 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASP q 111 " --> pdb=" O VAL q 83 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL q 85 " --> pdb=" O ASP q 111 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 't' and resid 29 through 31 Processing sheet with id=AB4, first strand: chain 't' and resid 35 through 39 removed outlier: 3.772A pdb=" N ARG t 35 " --> pdb=" O ARG t 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'y' and resid 2 through 8 removed outlier: 6.488A pdb=" N VAL y 21 " --> pdb=" O ARG y 35 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ARG y 35 " --> pdb=" O VAL y 21 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.744A pdb=" N ARG A 25 " --> pdb=" O CYS A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 473 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 841 hydrogen bonds 1328 hydrogen bond angles 0 basepair planarities 337 basepair parallelities 499 stacking parallelities Total time for adding SS restraints: 11.21 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4211 1.33 - 1.45: 16044 1.45 - 1.57: 14770 1.57 - 1.70: 2145 1.70 - 1.82: 76 Bond restraints: 37246 Sorted by residual: bond pdb=" N3 U g 471 " pdb=" C4 U g 471 " ideal model delta sigma weight residual 1.380 1.334 0.046 2.00e-02 2.50e+03 5.21e+00 bond pdb=" CG GLU n 23 " pdb=" CD GLU n 23 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.60e+00 bond pdb=" C6 A g 635 " pdb=" N6 A g 635 " ideal model delta sigma weight residual 1.335 1.302 0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" N3 U g 684 " pdb=" C4 U g 684 " ideal model delta sigma weight residual 1.380 1.349 0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C2 G g 741 " pdb=" N3 G g 741 " ideal model delta sigma weight residual 1.323 1.293 0.030 2.00e-02 2.50e+03 2.29e+00 ... (remaining 37241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 51718 2.06 - 4.12: 3450 4.12 - 6.18: 398 6.18 - 8.25: 31 8.25 - 10.31: 5 Bond angle restraints: 55602 Sorted by residual: angle pdb=" C ALA 2 14 " pdb=" CA ALA 2 14 " pdb=" CB ALA 2 14 " ideal model delta sigma weight residual 116.54 109.45 7.09 1.15e+00 7.56e-01 3.80e+01 angle pdb=" C3' A g1431 " pdb=" O3' A g1431 " pdb=" P G g1432 " ideal model delta sigma weight residual 119.70 126.60 -6.90 1.20e+00 6.94e-01 3.30e+01 angle pdb=" N GLU n 23 " pdb=" CA GLU n 23 " pdb=" CB GLU n 23 " ideal model delta sigma weight residual 110.16 117.22 -7.06 1.48e+00 4.57e-01 2.27e+01 angle pdb=" CA ALA 2 14 " pdb=" C ALA 2 14 " pdb=" N LEU 2 15 " ideal model delta sigma weight residual 119.52 116.03 3.49 7.90e-01 1.60e+00 1.95e+01 angle pdb=" C HIS n 94 " pdb=" CA HIS n 94 " pdb=" CB HIS n 94 " ideal model delta sigma weight residual 116.34 110.73 5.61 1.40e+00 5.10e-01 1.61e+01 ... (remaining 55597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 19177 35.14 - 70.27: 4298 70.27 - 105.41: 426 105.41 - 140.54: 3 140.54 - 175.68: 13 Dihedral angle restraints: 23917 sinusoidal: 19808 harmonic: 4109 Sorted by residual: dihedral pdb=" C4' C g 73 " pdb=" C3' C g 73 " pdb=" C2' C g 73 " pdb=" C1' C g 73 " ideal model delta sinusoidal sigma weight residual 36.34 -39.62 75.96 1 3.10e+00 1.04e-01 7.57e+02 dihedral pdb=" C4' A g 197 " pdb=" C3' A g 197 " pdb=" C2' A g 197 " pdb=" C1' A g 197 " ideal model delta sinusoidal sigma weight residual 36.34 -39.04 75.39 1 3.10e+00 1.04e-01 7.47e+02 dihedral pdb=" C4' U g 686 " pdb=" C3' U g 686 " pdb=" C2' U g 686 " pdb=" C1' U g 686 " ideal model delta sinusoidal sigma weight residual 36.35 -38.61 74.95 1 3.10e+00 1.04e-01 7.40e+02 ... (remaining 23914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 5380 0.082 - 0.165: 327 0.165 - 0.247: 1081 0.247 - 0.330: 285 0.330 - 0.412: 3 Chirality restraints: 7076 Sorted by residual: chirality pdb=" P G g1432 " pdb=" OP1 G g1432 " pdb=" OP2 G g1432 " pdb=" O5' G g1432 " both_signs ideal model delta sigma weight residual True 2.17 -2.59 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" P A g 687 " pdb=" OP1 A g 687 " pdb=" OP2 A g 687 " pdb=" O5' A g 687 " both_signs ideal model delta sigma weight residual True 2.17 -2.55 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" P U g 837 " pdb=" OP1 U g 837 " pdb=" OP2 U g 837 " pdb=" O5' U g 837 " both_signs ideal model delta sigma weight residual True 2.17 -2.52 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 7073 not shown) Planarity restraints: 3064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U g 603 " -0.021 2.00e-02 2.50e+03 2.63e-02 1.55e+01 pdb=" N1 U g 603 " 0.019 2.00e-02 2.50e+03 pdb=" C2 U g 603 " -0.014 2.00e-02 2.50e+03 pdb=" O2 U g 603 " 0.000 2.00e-02 2.50e+03 pdb=" N3 U g 603 " 0.014 2.00e-02 2.50e+03 pdb=" C4 U g 603 " 0.053 2.00e-02 2.50e+03 pdb=" O4 U g 603 " -0.047 2.00e-02 2.50e+03 pdb=" C5 U g 603 " -0.004 2.00e-02 2.50e+03 pdb=" C6 U g 603 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G g1494 " 0.008 2.00e-02 2.50e+03 1.82e-02 9.93e+00 pdb=" N9 G g1494 " -0.012 2.00e-02 2.50e+03 pdb=" C8 G g1494 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G g1494 " -0.007 2.00e-02 2.50e+03 pdb=" C5 G g1494 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G g1494 " 0.012 2.00e-02 2.50e+03 pdb=" O6 G g1494 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G g1494 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G g1494 " 0.047 2.00e-02 2.50e+03 pdb=" N2 G g1494 " -0.037 2.00e-02 2.50e+03 pdb=" N3 G g1494 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G g1494 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G g 690 " -0.038 2.00e-02 2.50e+03 1.77e-02 9.39e+00 pdb=" N9 G g 690 " 0.046 2.00e-02 2.50e+03 pdb=" C8 G g 690 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G g 690 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G g 690 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G g 690 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G g 690 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G g 690 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G g 690 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G g 690 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G g 690 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G g 690 " 0.001 2.00e-02 2.50e+03 ... (remaining 3061 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 598 2.56 - 3.14: 28613 3.14 - 3.73: 71992 3.73 - 4.31: 89054 4.31 - 4.90: 120235 Nonbonded interactions: 310492 Sorted by model distance: nonbonded pdb=" O6 G g1422 " pdb=" O2 U g1478 " model vdw 1.974 2.432 nonbonded pdb=" O2' G g1494 " pdb=" O4' U g1495 " model vdw 1.981 3.040 nonbonded pdb=" O2 U g 180 " pdb=" N7 A g 195 " model vdw 2.026 2.496 nonbonded pdb=" N2 G g 685 " pdb=" O ALA A 49 " model vdw 2.040 3.120 nonbonded pdb=" O2 C g 823 " pdb=" N2 G g 877 " model vdw 2.057 2.496 ... (remaining 310487 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 35.040 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37246 Z= 0.210 Angle : 1.011 10.308 55602 Z= 0.433 Chirality : 0.108 0.412 7076 Planarity : 0.005 0.063 3064 Dihedral : 28.323 175.681 21263 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 26.44 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.11 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -1.35 (0.22), residues: 1406 helix: 0.46 (0.23), residues: 494 sheet: -1.54 (0.34), residues: 214 loop : -1.69 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG q 121 TYR 0.038 0.002 TYR A 75 PHE 0.024 0.002 PHE l 19 TRP 0.010 0.001 TRP y 60 HIS 0.014 0.001 HIS q 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.21 (37246) covalent geometry : angle 1.01125 / 0.43 (55602) hydrogen bonds : bond 0.17038 / 11.31 ( 1305) hydrogen bonds : angle 6.48290 / 4.66 ( 2672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 53 MET cc_start: 0.9544 (ppp) cc_final: 0.9279 (ppp) REVERT: k 63 MET cc_start: 0.9240 (ppp) cc_final: 0.9029 (ppp) REVERT: l 19 PHE cc_start: 0.6170 (t80) cc_final: 0.5899 (t80) REVERT: n 59 TYR cc_start: 0.9190 (m-10) cc_final: 0.8970 (m-80) REVERT: n 61 LEU cc_start: 0.9465 (tt) cc_final: 0.9221 (tt) REVERT: n 98 GLU cc_start: 0.9135 (pm20) cc_final: 0.8878 (pm20) REVERT: p 110 MET cc_start: 0.8890 (mpp) cc_final: 0.8506 (mpp) REVERT: A 126 ILE cc_start: 0.5723 (tp) cc_final: 0.3987 (tp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1911 time to fit residues: 34.2971 Evaluate side-chains 79 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 HIS ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 117 GLN ** q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.024816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.016369 restraints weight = 705187.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.016966 restraints weight = 286532.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.017331 restraints weight = 182633.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.017466 restraints weight = 144742.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.017557 restraints weight = 131140.559| |-----------------------------------------------------------------------------| r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 37246 Z= 0.342 Angle : 1.518 20.473 55602 Z= 0.598 Chirality : 0.114 1.244 7076 Planarity : 0.006 0.065 3064 Dihedral : 27.491 178.931 18386 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 29.67 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.82 % Favored : 91.82 % Rotamer: Outliers : 0.08 % Allowed : 4.21 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 are not related in a simple way. whole: -1.32 (0.22), residues: 1406 helix: 0.52 (0.23), residues: 505 sheet: -1.50 (0.35), residues: 208 loop : -1.74 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG q 52 TYR 0.045 0.002 TYR A 75 PHE 0.010 0.002 PHE y 39 TRP 0.008 0.001 TRP y 60 HIS 0.023 0.002 HIS t 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.34 (37246) covalent geometry : angle 1.51812 / 0.60 (55602) hydrogen bonds : bond 0.12743 / 8.49 ( 1305) hydrogen bonds : angle 4.70897 / 3.27 ( 2672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 53 MET cc_start: 0.9492 (ppp) cc_final: 0.9285 (ppp) REVERT: k 11 GLN cc_start: 0.9161 (tp-100) cc_final: 0.8633 (pt0) REVERT: l 19 PHE cc_start: 0.6304 (t80) cc_final: 0.5995 (t80) REVERT: n 61 LEU cc_start: 0.9357 (tt) cc_final: 0.8880 (tt) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.2157 time to fit residues: 35.1832 Evaluate side-chains 73 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 166 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 186 optimal weight: 0.0050 chunk 194 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 overall best weight: 5.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 30 ASN ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 ASN ** q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.025200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.016658 restraints weight = 685418.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.017234 restraints weight = 271140.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.017659 restraints weight = 172793.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.017801 restraints weight = 135941.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.017898 restraints weight = 122838.203| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37246 Z= 0.223 Angle : 1.220 16.320 55602 Z= 0.483 Chirality : 0.090 0.962 7076 Planarity : 0.005 0.061 3064 Dihedral : 27.092 175.148 18386 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.61 % Favored : 93.03 % Rotamer: Outliers : 0.08 % Allowed : 4.13 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -0.90 (0.23), residues: 1406 helix: 1.03 (0.24), residues: 506 sheet: -1.43 (0.35), residues: 205 loop : -1.59 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG u 76 TYR 0.030 0.002 TYR A 75 PHE 0.021 0.001 PHE u 42 TRP 0.008 0.001 TRP y 60 HIS 0.013 0.002 HIS t 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.22 (37246) covalent geometry : angle 1.21967 / 0.48 (55602) hydrogen bonds : bond 0.10868 / 7.29 ( 1305) hydrogen bonds : angle 4.10102 / 2.86 ( 2672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 53 MET cc_start: 0.9432 (ppp) cc_final: 0.9214 (ppp) REVERT: n 59 TYR cc_start: 0.9037 (m-80) cc_final: 0.8716 (m-80) REVERT: n 61 LEU cc_start: 0.9406 (tt) cc_final: 0.8909 (tt) REVERT: n 88 MET cc_start: 0.8534 (tmm) cc_final: 0.8319 (tmm) REVERT: n 90 MET cc_start: 0.8937 (mmm) cc_final: 0.8556 (mmm) REVERT: p 26 MET cc_start: 0.6862 (mpp) cc_final: 0.5696 (mpp) REVERT: p 110 MET cc_start: 0.8719 (mpp) cc_final: 0.8277 (mpp) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.2298 time to fit residues: 36.9181 Evaluate side-chains 72 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 223 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 149 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 69 ASN ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 ASN ** q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.025025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.016628 restraints weight = 679223.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.017198 restraints weight = 274608.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.017594 restraints weight = 175178.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.017705 restraints weight = 137755.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.017870 restraints weight = 126263.433| |-----------------------------------------------------------------------------| r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 37246 Z= 0.228 Angle : 1.203 14.751 55602 Z= 0.476 Chirality : 0.087 0.982 7076 Planarity : 0.005 0.057 3064 Dihedral : 26.856 178.886 18386 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.18 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 are not related in a simple way. whole: -0.92 (0.22), residues: 1406 helix: 1.05 (0.24), residues: 506 sheet: -1.31 (0.35), residues: 204 loop : -1.69 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG u 76 TYR 0.038 0.002 TYR A 75 PHE 0.017 0.001 PHE n 80 TRP 0.007 0.001 TRP n 42 HIS 0.010 0.002 HIS t 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.23 (37246) covalent geometry : angle 1.20318 / 0.48 (55602) hydrogen bonds : bond 0.10812 / 7.07 ( 1305) hydrogen bonds : angle 4.08825 / 2.86 ( 2672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 53 MET cc_start: 0.9477 (ppp) cc_final: 0.9248 (ppp) REVERT: n 59 TYR cc_start: 0.9039 (m-80) cc_final: 0.8612 (m-80) REVERT: n 61 LEU cc_start: 0.9371 (tt) cc_final: 0.8961 (tt) REVERT: n 90 MET cc_start: 0.9139 (mmm) cc_final: 0.8828 (mmm) REVERT: p 110 MET cc_start: 0.8742 (mpp) cc_final: 0.8155 (pmm) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2191 time to fit residues: 33.6749 Evaluate side-chains 71 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 148 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 239 optimal weight: 40.0000 chunk 73 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 185 optimal weight: 30.0000 chunk 161 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.024571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.016350 restraints weight = 704225.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.016892 restraints weight = 285517.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.017135 restraints weight = 182383.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.017311 restraints weight = 151152.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.017327 restraints weight = 137129.737| |-----------------------------------------------------------------------------| r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 37246 Z= 0.402 Angle : 1.454 16.060 55602 Z= 0.573 Chirality : 0.096 1.132 7076 Planarity : 0.007 0.078 3064 Dihedral : 27.108 179.607 18386 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 39.22 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.89 % Favored : 90.61 % Rotamer: Outliers : 0.17 % Allowed : 4.38 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 are not related in a simple way. whole: -1.70 (0.21), residues: 1406 helix: 0.23 (0.22), residues: 508 sheet: -1.90 (0.34), residues: 195 loop : -1.94 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG u 53 TYR 0.054 0.003 TYR A 75 PHE 0.026 0.002 PHE k 94 TRP 0.010 0.002 TRP n 42 HIS 0.013 0.003 HIS t 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00804 / 0.40 (37246) covalent geometry : angle 1.45364 / 0.57 (55602) hydrogen bonds : bond 0.14597 / 9.48 ( 1305) hydrogen bonds : angle 4.65629 / 3.25 ( 2672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: l 19 PHE cc_start: 0.7273 (t80) cc_final: 0.6802 (t80) REVERT: n 90 MET cc_start: 0.8804 (mmm) cc_final: 0.8431 (mmm) outliers start: 2 outliers final: 1 residues processed: 85 average time/residue: 0.2435 time to fit residues: 33.1840 Evaluate side-chains 66 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 28 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.024774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.016458 restraints weight = 682236.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.017002 restraints weight = 276441.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.017245 restraints weight = 178479.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.017423 restraints weight = 149136.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.017445 restraints weight = 135939.744| |-----------------------------------------------------------------------------| r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 37246 Z= 0.213 Angle : 1.190 14.863 55602 Z= 0.473 Chirality : 0.087 0.981 7076 Planarity : 0.005 0.058 3064 Dihedral : 26.868 178.432 18386 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.97 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 are not related in a simple way. whole: -1.13 (0.22), residues: 1406 helix: 0.77 (0.23), residues: 505 sheet: -1.48 (0.36), residues: 197 loop : -1.69 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG k 53 TYR 0.036 0.002 TYR A 75 PHE 0.028 0.002 PHE n 80 TRP 0.010 0.001 TRP y 60 HIS 0.009 0.001 HIS t 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.21 (37246) covalent geometry : angle 1.18986 / 0.47 (55602) hydrogen bonds : bond 0.10661 / 6.97 ( 1305) hydrogen bonds : angle 4.19749 / 2.95 ( 2672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 53 MET cc_start: 0.9470 (ppp) cc_final: 0.9259 (ppp) REVERT: l 19 PHE cc_start: 0.8214 (t80) cc_final: 0.7583 (t80) REVERT: n 59 TYR cc_start: 0.9280 (m-10) cc_final: 0.9080 (m-80) REVERT: n 61 LEU cc_start: 0.9570 (tt) cc_final: 0.9337 (tt) REVERT: n 88 MET cc_start: 0.8469 (tmm) cc_final: 0.7897 (tmm) REVERT: n 90 MET cc_start: 0.9157 (mmm) cc_final: 0.8861 (mmm) REVERT: p 110 MET cc_start: 0.8780 (mpp) cc_final: 0.8552 (mpp) REVERT: t 56 LEU cc_start: 0.9147 (tp) cc_final: 0.8924 (tp) REVERT: A 126 ILE cc_start: 0.7603 (tp) cc_final: 0.7393 (tp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2262 time to fit residues: 35.7556 Evaluate side-chains 74 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 225 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 148 optimal weight: 30.0000 chunk 3 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 234 optimal weight: 20.0000 chunk 223 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 196 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.024720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.016417 restraints weight = 691532.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.016964 restraints weight = 276284.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.017210 restraints weight = 175469.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.017400 restraints weight = 146464.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.017422 restraints weight = 131907.960| |-----------------------------------------------------------------------------| r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 37246 Z= 0.247 Angle : 1.215 14.504 55602 Z= 0.482 Chirality : 0.086 1.022 7076 Planarity : 0.005 0.056 3064 Dihedral : 26.827 178.979 18386 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 24.33 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.40 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 are not related in a simple way. whole: -1.18 (0.22), residues: 1406 helix: 0.77 (0.23), residues: 507 sheet: -1.60 (0.34), residues: 204 loop : -1.73 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 2 46 TYR 0.030 0.002 TYR A 75 PHE 0.015 0.002 PHE 3 30 TRP 0.007 0.001 TRP y 60 HIS 0.009 0.002 HIS u 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.25 (37246) covalent geometry : angle 1.21463 / 0.48 (55602) hydrogen bonds : bond 0.10937 / 7.17 ( 1305) hydrogen bonds : angle 4.17160 / 2.93 ( 2672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 63 MET cc_start: 0.9358 (ppp) cc_final: 0.9137 (ppp) REVERT: l 19 PHE cc_start: 0.8008 (t80) cc_final: 0.7373 (t80) REVERT: n 88 MET cc_start: 0.8354 (tmm) cc_final: 0.7801 (tmm) REVERT: n 90 MET cc_start: 0.9115 (mmm) cc_final: 0.8824 (mmm) REVERT: p 110 MET cc_start: 0.8691 (mpp) cc_final: 0.8337 (mpp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2306 time to fit residues: 35.3723 Evaluate side-chains 71 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 137 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 217 optimal weight: 30.0000 chunk 98 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.024639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.016426 restraints weight = 700198.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.016972 restraints weight = 280440.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.017215 restraints weight = 178645.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.017417 restraints weight = 148278.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.017431 restraints weight = 132628.889| |-----------------------------------------------------------------------------| r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 37246 Z= 0.284 Angle : 1.261 14.816 55602 Z= 0.500 Chirality : 0.087 1.102 7076 Planarity : 0.006 0.063 3064 Dihedral : 26.849 179.374 18386 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 28.04 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.46 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 are not related in a simple way. whole: -1.32 (0.22), residues: 1406 helix: 0.65 (0.23), residues: 505 sheet: -1.68 (0.34), residues: 204 loop : -1.80 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG n 24 TYR 0.025 0.002 TYR A 75 PHE 0.033 0.002 PHE 3 30 TRP 0.006 0.001 TRP n 42 HIS 0.010 0.002 HIS t 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.28 (37246) covalent geometry : angle 1.26062 / 0.50 (55602) hydrogen bonds : bond 0.11338 / 7.39 ( 1305) hydrogen bonds : angle 4.29479 / 3.01 ( 2672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 63 MET cc_start: 0.9401 (ppp) cc_final: 0.9195 (ppp) REVERT: l 19 PHE cc_start: 0.8070 (t80) cc_final: 0.7387 (t80) REVERT: n 59 TYR cc_start: 0.9355 (m-10) cc_final: 0.9118 (m-80) REVERT: n 88 MET cc_start: 0.8199 (tmm) cc_final: 0.7638 (tmm) REVERT: n 90 MET cc_start: 0.9040 (mmm) cc_final: 0.8705 (mmm) REVERT: p 110 MET cc_start: 0.8658 (mpp) cc_final: 0.8331 (mpp) REVERT: t 56 LEU cc_start: 0.9126 (tp) cc_final: 0.8919 (tp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2443 time to fit residues: 32.8888 Evaluate side-chains 71 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 227 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 21 optimal weight: 0.2980 chunk 221 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 222 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 161 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 30 HIS ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 21 HIS ** 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 = 0.2838 r_free = 0.2838 target = 0.024935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.016713 restraints weight = 665570.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.017267 restraints weight = 268972.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.017512 restraints weight = 171454.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.017723 restraints weight = 142300.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.017890 restraints weight = 127781.389| |-----------------------------------------------------------------------------| r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 37246 Z= 0.193 Angle : 1.141 14.004 55602 Z= 0.454 Chirality : 0.083 0.948 7076 Planarity : 0.005 0.054 3064 Dihedral : 26.674 179.404 18386 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.04 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -1.03 (0.22), residues: 1406 helix: 0.96 (0.24), residues: 505 sheet: -1.44 (0.35), residues: 202 loop : -1.73 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG u 76 TYR 0.019 0.002 TYR u 77 PHE 0.022 0.001 PHE 3 30 TRP 0.009 0.001 TRP y 60 HIS 0.010 0.001 HIS t 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (37246) covalent geometry : angle 1.14055 / 0.45 (55602) hydrogen bonds : bond 0.09880 / 6.48 ( 1305) hydrogen bonds : angle 4.08546 / 2.90 ( 2672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 53 MET cc_start: 0.9195 (mmt) cc_final: 0.8761 (mmt) REVERT: k 110 MET cc_start: 0.8222 (tmm) cc_final: 0.7956 (tmm) REVERT: k 146 MET cc_start: 0.6175 (tpt) cc_final: 0.5734 (tpp) REVERT: l 19 PHE cc_start: 0.8125 (t80) cc_final: 0.7454 (t80) REVERT: n 59 TYR cc_start: 0.9407 (m-10) cc_final: 0.9148 (m-80) REVERT: n 88 MET cc_start: 0.8319 (tmm) cc_final: 0.7775 (tmm) REVERT: n 90 MET cc_start: 0.9145 (mmm) cc_final: 0.8943 (mmm) REVERT: p 110 MET cc_start: 0.8753 (mpp) cc_final: 0.8394 (mpp) REVERT: t 56 LEU cc_start: 0.9105 (tp) cc_final: 0.8890 (tp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2099 time to fit residues: 32.5661 Evaluate side-chains 70 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 46 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 219 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 49 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 232 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 240 optimal weight: 10.0000 overall best weight: 6.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.024735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.016587 restraints weight = 680152.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.017163 restraints weight = 276926.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.017402 restraints weight = 176296.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.017605 restraints weight = 145722.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.017765 restraints weight = 130498.341| |-----------------------------------------------------------------------------| r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 37246 Z= 0.231 Angle : 1.176 14.080 55602 Z= 0.469 Chirality : 0.083 0.985 7076 Planarity : 0.005 0.049 3064 Dihedral : 26.686 179.813 18386 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 23.48 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.61 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 are not related in a simple way. whole: -1.16 (0.22), residues: 1406 helix: 0.82 (0.23), residues: 506 sheet: -1.58 (0.34), residues: 206 loop : -1.75 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG n 24 TYR 0.022 0.002 TYR A 75 PHE 0.021 0.002 PHE 3 30 TRP 0.006 0.001 TRP q 43 HIS 0.011 0.001 HIS t 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.23 (37246) covalent geometry : angle 1.17606 / 0.47 (55602) hydrogen bonds : bond 0.10300 / 6.77 ( 1305) hydrogen bonds : angle 4.17705 / 2.95 ( 2672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 63 MET cc_start: 0.9405 (ppp) cc_final: 0.9199 (ppp) REVERT: l 19 PHE cc_start: 0.8227 (t80) cc_final: 0.7506 (t80) REVERT: n 59 TYR cc_start: 0.9402 (m-10) cc_final: 0.9137 (m-80) REVERT: p 110 MET cc_start: 0.8652 (mpp) cc_final: 0.8292 (mpp) REVERT: q 60 PHE cc_start: 0.9332 (t80) cc_final: 0.8938 (p90) REVERT: t 56 LEU cc_start: 0.9138 (tp) cc_final: 0.8904 (tp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2266 time to fit residues: 32.0332 Evaluate side-chains 67 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 225 optimal weight: 2.9990 chunk 176 optimal weight: 30.0000 chunk 104 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 238 optimal weight: 40.0000 chunk 161 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.024933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.016727 restraints weight = 670007.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.017292 restraints weight = 270218.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.017685 restraints weight = 172805.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.017821 restraints weight = 136252.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.017922 restraints weight = 122776.733| |-----------------------------------------------------------------------------| r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 37246 Z= 0.196 Angle : 1.135 15.407 55602 Z= 0.452 Chirality : 0.081 0.913 7076 Planarity : 0.005 0.049 3064 Dihedral : 26.650 178.199 18386 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.54 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -1.04 (0.22), residues: 1406 helix: 0.90 (0.24), residues: 507 sheet: -1.53 (0.34), residues: 206 loop : -1.66 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG n 24 TYR 0.019 0.001 TYR A 75 PHE 0.023 0.002 PHE 3 30 TRP 0.007 0.001 TRP y 60 HIS 0.010 0.001 HIS t 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.20 (37246) covalent geometry : angle 1.13471 / 0.45 (55602) hydrogen bonds : bond 0.09665 / 6.36 ( 1305) hydrogen bonds : angle 4.12508 / 2.92 ( 2672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5760.47 seconds wall clock time: 100 minutes 53.90 seconds (6053.90 seconds total)