Starting phenix.real_space_refine on Sat Feb 7 13:09:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsh_36620/02_2026/8jsh_36620.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsh_36620/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jsh_36620/02_2026/8jsh_36620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsh_36620/02_2026/8jsh_36620.map" model { file = "/net/cci-nas-00/data/ceres_data/8jsh_36620/02_2026/8jsh_36620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsh_36620/02_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-2.0-5952/lib/python3.9/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: {'RNA': 1074} Modifications used: {'5*END': 1, 'rna2p_pur': 86, 'rna2p_pyr': 55, 'rna3p_pur': 531, 'rna3p_pyr': 402} Link IDs: {'rna2p': 140, 'rna3p': 933} Chain breaks: 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: 5.89, per 1000 atoms: 0.17 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: 2.69 Conformation dependent library (CDL) restraints added in 667.8 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: 6.01 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: 11.82 Time building geometry restraints manager: 3.76 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: 54299 2.06 - 4.12: 1136 4.12 - 6.18: 134 6.18 - 8.25: 28 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=" 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=" C3' A g1431 " pdb=" O3' A g1431 " pdb=" P G g1432 " ideal model delta sigma weight residual 120.20 126.60 -6.40 1.50e+00 4.44e-01 1.82e+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 - 35.81: 20350 35.81 - 71.62: 3141 71.62 - 107.43: 396 107.43 - 143.24: 13 143.24 - 179.05: 17 Dihedral angle restraints: 23917 sinusoidal: 19808 harmonic: 4109 Sorted by residual: dihedral pdb=" C5' U g1527 " pdb=" C4' U g1527 " pdb=" C3' U g1527 " pdb=" O3' U g1527 " ideal model delta sinusoidal sigma weight residual 147.00 77.52 69.48 1 8.00e+00 1.56e-02 9.74e+01 dihedral pdb=" C5' A g 572 " pdb=" C4' A g 572 " pdb=" C3' A g 572 " pdb=" O3' A g 572 " ideal model delta sinusoidal sigma weight residual 147.00 77.86 69.14 1 8.00e+00 1.56e-02 9.66e+01 dihedral pdb=" C5' G g 836 " pdb=" C4' G g 836 " pdb=" C3' G g 836 " pdb=" O3' G g 836 " ideal model delta sinusoidal sigma weight residual 147.00 78.27 68.73 1 8.00e+00 1.56e-02 9.56e+01 ... (remaining 23914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 6559 0.071 - 0.143: 456 0.143 - 0.214: 50 0.214 - 0.285: 8 0.285 - 0.356: 3 Chirality restraints: 7076 Sorted by residual: chirality pdb=" C3' G g 836 " pdb=" C4' G g 836 " pdb=" O3' G g 836 " pdb=" C2' G g 836 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C3' A g 572 " pdb=" C4' A g 572 " pdb=" O3' A g 572 " pdb=" C2' A g 572 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C3' U g1527 " pdb=" C4' U g1527 " pdb=" O3' U g1527 " pdb=" C2' U g1527 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.29 2.00e-01 2.50e+01 2.07e+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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 36.640 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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= 0.196 Angle : 0.728 10.308 55602 Z= 0.383 Chirality : 0.039 0.356 7076 Planarity : 0.005 0.063 3064 Dihedral : 26.039 179.048 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 covalent geometry : bond 0.00358 (37246) covalent geometry : angle 0.72843 (55602) hydrogen bonds : bond 0.17038 ( 1305) hydrogen bonds : angle 6.48290 ( 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 : 0.726 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: 0.2062 time to fit residues: 36.8621 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 : 0.681 ------------------------------------------------------------------------------- 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: 20.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 235 optimal weight: 20.0000 overall best weight: 14.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 HIS ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 HIS l 88 ASN ** n 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 37 ASN p 117 GLN ** q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.024411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.016000 restraints weight = 713762.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.016528 restraints weight = 295991.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.016752 restraints weight = 191557.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.016956 restraints weight = 158893.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.017089 restraints weight = 141933.220| |-----------------------------------------------------------------------------| r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 37246 Z= 0.392 Angle : 0.952 11.311 55602 Z= 0.466 Chirality : 0.047 0.271 7076 Planarity : 0.007 0.069 3064 Dihedral : 27.140 179.483 18386 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 37.76 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.82 % Favored : 90.75 % Rotamer: Outliers : 0.42 % Allowed : 6.07 % Favored : 93.51 % 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: -1.76 (0.21), residues: 1406 helix: 0.03 (0.22), residues: 507 sheet: -1.67 (0.34), residues: 205 loop : -1.94 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG u 53 TYR 0.054 0.003 TYR A 75 PHE 0.015 0.002 PHE l 106 TRP 0.008 0.002 TRP y 60 HIS 0.025 0.003 HIS t 76 Details of bonding type rmsd covalent geometry : bond 0.00731 (37246) covalent geometry : angle 0.95170 (55602) hydrogen bonds : bond 0.14144 ( 1305) hydrogen bonds : angle 4.88219 ( 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 98 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.693 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: l 19 PHE cc_start: 0.6190 (t80) cc_final: 0.5825 (t80) REVERT: n 61 LEU cc_start: 0.9264 (tt) cc_final: 0.8857 (tt) outliers start: 5 outliers final: 1 residues processed: 98 average time/residue: 0.2387 time to fit residues: 37.9353 Evaluate side-chains 74 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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: 7.9990 chunk 147 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 160 optimal weight: 0.0980 chunk 104 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 overall best weight: 6.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 30 ASN ** 2 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 69 ASN ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.024512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.015994 restraints weight = 694467.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.016540 restraints weight = 281896.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.016765 restraints weight = 181412.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.016981 restraints weight = 151292.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.017158 restraints weight = 135863.575| |-----------------------------------------------------------------------------| r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 37246 Z= 0.204 Angle : 0.706 10.674 55602 Z= 0.354 Chirality : 0.039 0.256 7076 Planarity : 0.005 0.061 3064 Dihedral : 26.614 179.426 18386 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.04 % Favored : 92.53 % Rotamer: Outliers : 0.08 % Allowed : 3.62 % Favored : 96.29 % 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: -1.21 (0.22), residues: 1406 helix: 0.74 (0.23), residues: 506 sheet: -1.54 (0.34), residues: 208 loop : -1.76 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG u 53 TYR 0.036 0.002 TYR A 75 PHE 0.012 0.001 PHE u 42 TRP 0.009 0.001 TRP y 60 HIS 0.013 0.002 HIS t 76 Details of bonding type rmsd covalent geometry : bond 0.00378 (37246) covalent geometry : angle 0.70584 (55602) hydrogen bonds : bond 0.10181 ( 1305) hydrogen bonds : angle 4.19115 ( 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 100 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 53 MET cc_start: 0.9450 (ppp) cc_final: 0.9245 (ppp) REVERT: k 11 GLN cc_start: 0.9148 (tp-100) cc_final: 0.8639 (pt0) REVERT: n 61 LEU cc_start: 0.9317 (tt) cc_final: 0.8786 (tt) REVERT: p 26 MET cc_start: 0.7120 (mpp) cc_final: 0.6634 (mpp) REVERT: p 110 MET cc_start: 0.8758 (mpp) cc_final: 0.8298 (mpp) REVERT: A 126 ILE cc_start: 0.6410 (tp) cc_final: 0.5728 (tp) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.2071 time to fit residues: 33.7052 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 : 0.687 ------------------------------------------------------------------------------- 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: 1.9990 chunk 241 optimal weight: 8.9990 chunk 183 optimal weight: 20.0000 chunk 127 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 229 optimal weight: 30.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 30 HIS ** 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 = 0.2798 r_free = 0.2798 target = 0.024301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.015897 restraints weight = 695721.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.016415 restraints weight = 287123.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.016631 restraints weight = 185098.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.016839 restraints weight = 154094.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.017021 restraints weight = 138194.596| |-----------------------------------------------------------------------------| r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 37246 Z= 0.275 Angle : 0.766 11.265 55602 Z= 0.382 Chirality : 0.041 0.291 7076 Planarity : 0.005 0.063 3064 Dihedral : 26.713 176.807 18386 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 27.90 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.61 % Favored : 90.97 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % 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: -1.41 (0.22), residues: 1406 helix: 0.48 (0.23), residues: 508 sheet: -1.52 (0.35), residues: 198 loop : -1.86 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG u 53 TYR 0.045 0.002 TYR A 75 PHE 0.012 0.002 PHE n 80 TRP 0.007 0.001 TRP y 60 HIS 0.011 0.002 HIS t 76 Details of bonding type rmsd covalent geometry : bond 0.00513 (37246) covalent geometry : angle 0.76630 (55602) hydrogen bonds : bond 0.11516 ( 1305) hydrogen bonds : angle 4.32062 ( 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 86 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.723 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: 3 53 MET cc_start: 0.9446 (ppp) cc_final: 0.9238 (ppp) REVERT: l 19 PHE cc_start: 0.6822 (t80) cc_final: 0.6330 (t80) REVERT: p 110 MET cc_start: 0.8603 (mpp) cc_final: 0.8173 (mpp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2402 time to fit residues: 33.3541 Evaluate side-chains 77 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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: 9.9990 chunk 56 optimal weight: 20.0000 chunk 239 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 185 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 131 ASN ** 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 = 0.2802 r_free = 0.2802 target = 0.024286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.015852 restraints weight = 691192.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.016379 restraints weight = 283665.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.016730 restraints weight = 182837.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.016850 restraints weight = 146647.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.016927 restraints weight = 133658.677| |-----------------------------------------------------------------------------| r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37246 Z= 0.225 Angle : 0.706 10.813 55602 Z= 0.354 Chirality : 0.038 0.281 7076 Planarity : 0.005 0.060 3064 Dihedral : 26.536 175.104 18386 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 23.37 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.82 % Favored : 91.75 % Rotamer: Outliers : 0.08 % Allowed : 3.29 % Favored : 96.63 % 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: -1.29 (0.22), residues: 1406 helix: 0.64 (0.23), residues: 504 sheet: -1.52 (0.36), residues: 197 loop : -1.80 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG u 53 TYR 0.039 0.002 TYR A 75 PHE 0.010 0.002 PHE n 80 TRP 0.007 0.001 TRP y 60 HIS 0.008 0.002 HIS t 76 Details of bonding type rmsd covalent geometry : bond 0.00419 (37246) covalent geometry : angle 0.70610 (55602) hydrogen bonds : bond 0.10548 ( 1305) hydrogen bonds : angle 4.09373 ( 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 98 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.675 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: l 19 PHE cc_start: 0.7970 (t80) cc_final: 0.7404 (t80) REVERT: n 90 MET cc_start: 0.9073 (mmp) cc_final: 0.8791 (mmm) REVERT: p 110 MET cc_start: 0.8711 (mpp) cc_final: 0.8287 (mpp) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.2326 time to fit residues: 37.2418 Evaluate side-chains 77 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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: 0.5980 chunk 150 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 205 optimal weight: 6.9990 chunk 161 optimal weight: 0.0010 chunk 44 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 243 optimal weight: 0.5980 overall best weight: 3.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.024692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.016126 restraints weight = 678114.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.016691 restraints weight = 273089.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.017055 restraints weight = 175291.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.017175 restraints weight = 140536.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.017271 restraints weight = 127686.233| |-----------------------------------------------------------------------------| r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37246 Z= 0.145 Angle : 0.630 9.864 55602 Z= 0.320 Chirality : 0.035 0.257 7076 Planarity : 0.004 0.053 3064 Dihedral : 26.161 173.502 18386 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.33 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -1.07 (0.22), residues: 1406 helix: 0.93 (0.24), residues: 506 sheet: -1.32 (0.36), residues: 195 loop : -1.81 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG n 38 TYR 0.029 0.001 TYR A 75 PHE 0.019 0.001 PHE n 80 TRP 0.008 0.001 TRP y 60 HIS 0.009 0.001 HIS t 76 Details of bonding type rmsd covalent geometry : bond 0.00267 (37246) covalent geometry : angle 0.63003 (55602) hydrogen bonds : bond 0.09750 ( 1305) hydrogen bonds : angle 3.91514 ( 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 103 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.730 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: l 19 PHE cc_start: 0.7758 (t80) cc_final: 0.7158 (t80) REVERT: n 62 MET cc_start: 0.9541 (tpt) cc_final: 0.9306 (tpt) REVERT: p 110 MET cc_start: 0.8806 (mpp) cc_final: 0.8482 (mpp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2387 time to fit residues: 39.6415 Evaluate side-chains 76 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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: 9.9990 chunk 31 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 234 optimal weight: 20.0000 chunk 223 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 196 optimal weight: 0.0270 overall best weight: 8.6048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 99 ASN ** p 17 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 = 0.2800 r_free = 0.2800 target = 0.024332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.015906 restraints weight = 696551.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.016455 restraints weight = 282747.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.016683 restraints weight = 182448.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.016857 restraints weight = 152337.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 74)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.017029 restraints weight = 138951.445| |-----------------------------------------------------------------------------| r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 37246 Z= 0.240 Angle : 0.708 10.226 55602 Z= 0.356 Chirality : 0.038 0.275 7076 Planarity : 0.005 0.057 3064 Dihedral : 26.405 173.942 18386 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 24.31 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.25 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: -1.21 (0.22), residues: 1406 helix: 0.81 (0.23), residues: 504 sheet: -1.48 (0.35), residues: 194 loop : -1.85 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG n 24 TYR 0.042 0.002 TYR A 75 PHE 0.013 0.002 PHE l 106 TRP 0.013 0.002 TRP n 42 HIS 0.009 0.002 HIS t 76 Details of bonding type rmsd covalent geometry : bond 0.00447 (37246) covalent geometry : angle 0.70822 (55602) hydrogen bonds : bond 0.10650 ( 1305) hydrogen bonds : angle 4.05888 ( 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 87 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.761 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: 0.8009 (t80) cc_final: 0.7371 (t80) REVERT: p 110 MET cc_start: 0.8736 (mpp) cc_final: 0.8373 (mpp) REVERT: t 56 LEU cc_start: 0.9134 (tp) cc_final: 0.8925 (tp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2565 time to fit residues: 35.3257 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 : 0.735 ------------------------------------------------------------------------------- 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: 5.9990 chunk 126 optimal weight: 30.0000 chunk 217 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 218 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 30 HIS ** k 131 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.024587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.016056 restraints weight = 684568.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.016605 restraints weight = 276948.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.016831 restraints weight = 177807.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.017019 restraints weight = 148860.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.017213 restraints weight = 134863.110| |-----------------------------------------------------------------------------| r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37246 Z= 0.158 Angle : 0.638 9.694 55602 Z= 0.323 Chirality : 0.036 0.271 7076 Planarity : 0.004 0.055 3064 Dihedral : 26.176 173.768 18386 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.25 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: -1.06 (0.22), residues: 1406 helix: 0.96 (0.24), residues: 506 sheet: -1.47 (0.35), residues: 197 loop : -1.76 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG u 53 TYR 0.034 0.002 TYR A 75 PHE 0.021 0.001 PHE 3 30 TRP 0.008 0.001 TRP y 60 HIS 0.008 0.001 HIS t 76 Details of bonding type rmsd covalent geometry : bond 0.00293 (37246) covalent geometry : angle 0.63766 (55602) hydrogen bonds : bond 0.09508 ( 1305) hydrogen bonds : angle 3.90644 ( 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 92 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.670 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: l 19 PHE cc_start: 0.7916 (t80) cc_final: 0.7265 (t80) REVERT: n 59 TYR cc_start: 0.9316 (m-10) cc_final: 0.9101 (m-80) REVERT: n 80 PHE cc_start: 0.9726 (m-80) cc_final: 0.9526 (m-80) REVERT: p 110 MET cc_start: 0.8680 (mpp) cc_final: 0.8357 (mpp) REVERT: q 60 PHE cc_start: 0.9453 (t80) cc_final: 0.9140 (p90) REVERT: t 56 LEU cc_start: 0.9110 (tp) cc_final: 0.8898 (tp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2408 time to fit residues: 35.2286 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 : 0.659 ------------------------------------------------------------------------------- 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: 10.0000 chunk 105 optimal weight: 30.0000 chunk 21 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 222 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 9 optimal weight: 40.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 73 HIS ** k 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 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 = 0.2795 r_free = 0.2795 target = 0.024286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.015884 restraints weight = 694535.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.016418 restraints weight = 281485.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.016705 restraints weight = 186978.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.016834 restraints weight = 150048.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.016870 restraints weight = 134427.757| |-----------------------------------------------------------------------------| r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37246 Z= 0.240 Angle : 0.715 11.050 55602 Z= 0.359 Chirality : 0.038 0.285 7076 Planarity : 0.005 0.057 3064 Dihedral : 26.377 173.768 18386 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.32 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -1.19 (0.22), residues: 1406 helix: 0.86 (0.24), residues: 505 sheet: -1.48 (0.36), residues: 188 loop : -1.87 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG l 103 TYR 0.046 0.002 TYR A 75 PHE 0.039 0.002 PHE 3 30 TRP 0.005 0.001 TRP y 60 HIS 0.020 0.002 HIS t 76 Details of bonding type rmsd covalent geometry : bond 0.00447 (37246) covalent geometry : angle 0.71493 (55602) hydrogen bonds : bond 0.10528 ( 1305) hydrogen bonds : angle 4.13251 ( 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 87 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.844 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: l 19 PHE cc_start: 0.8100 (t80) cc_final: 0.7419 (t80) REVERT: n 59 TYR cc_start: 0.9341 (m-10) cc_final: 0.9104 (m-80) REVERT: n 88 MET cc_start: 0.7981 (tmm) cc_final: 0.7773 (tmm) REVERT: p 110 MET cc_start: 0.8682 (mpp) cc_final: 0.8337 (mpp) REVERT: q 60 PHE cc_start: 0.9467 (t80) cc_final: 0.9151 (p90) REVERT: t 56 LEU cc_start: 0.9133 (tp) cc_final: 0.8911 (tp) REVERT: A 68 MET cc_start: 0.3966 (tpt) cc_final: 0.3469 (tpt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2387 time to fit residues: 33.7418 Evaluate side-chains 68 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 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 46 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 232 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 21 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.024474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.015954 restraints weight = 693369.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.016503 restraints weight = 279855.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.016749 restraints weight = 180365.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.017051 restraints weight = 150621.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.017109 restraints weight = 131461.638| |-----------------------------------------------------------------------------| r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37246 Z= 0.187 Angle : 0.665 10.424 55602 Z= 0.336 Chirality : 0.036 0.280 7076 Planarity : 0.005 0.055 3064 Dihedral : 26.237 174.103 18386 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.33 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 0.89 (0.24), residues: 506 sheet: -1.50 (0.35), residues: 190 loop : -1.81 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG k 53 TYR 0.044 0.002 TYR A 75 PHE 0.028 0.002 PHE 3 30 TRP 0.008 0.001 TRP y 60 HIS 0.012 0.001 HIS t 76 Details of bonding type rmsd covalent geometry : bond 0.00348 (37246) covalent geometry : angle 0.66451 (55602) hydrogen bonds : bond 0.09665 ( 1305) hydrogen bonds : angle 3.99484 ( 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 89 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.770 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: l 19 PHE cc_start: 0.8049 (t80) cc_final: 0.7322 (t80) REVERT: n 59 TYR cc_start: 0.9328 (m-10) cc_final: 0.9101 (m-80) REVERT: p 110 MET cc_start: 0.8661 (mpp) cc_final: 0.8313 (mpp) REVERT: q 60 PHE cc_start: 0.9471 (t80) cc_final: 0.9143 (p90) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2388 time to fit residues: 34.6216 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 : 0.719 ------------------------------------------------------------------------------- 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: 0.0870 chunk 176 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 238 optimal weight: 30.0000 chunk 161 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 32 optimal weight: 30.0000 chunk 11 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.024505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.015993 restraints weight = 689281.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.016546 restraints weight = 279459.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.016772 restraints weight = 179965.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.016992 restraints weight = 149609.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.017189 restraints weight = 135102.733| |-----------------------------------------------------------------------------| r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37246 Z= 0.176 Angle : 0.656 10.394 55602 Z= 0.332 Chirality : 0.036 0.282 7076 Planarity : 0.004 0.054 3064 Dihedral : 26.183 174.022 18386 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.82 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.88 (0.24), residues: 507 sheet: -1.48 (0.36), residues: 190 loop : -1.80 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG k 53 TYR 0.043 0.002 TYR A 75 PHE 0.028 0.001 PHE 3 30 TRP 0.007 0.001 TRP y 60 HIS 0.011 0.001 HIS t 76 Details of bonding type rmsd covalent geometry : bond 0.00328 (37246) covalent geometry : angle 0.65639 (55602) hydrogen bonds : bond 0.09377 ( 1305) hydrogen bonds : angle 4.02430 ( 2672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6228.70 seconds wall clock time: 108 minutes 56.60 seconds (6536.60 seconds total)