Starting phenix.real_space_refine on Fri Mar 22 17:19:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsh_36620/03_2024/8jsh_36620.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsh_36620/03_2024/8jsh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsh_36620/03_2024/8jsh_36620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsh_36620/03_2024/8jsh_36620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsh_36620/03_2024/8jsh_36620.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsh_36620/03_2024/8jsh_36620.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 Residue "k GLU 12": "OE1" <-> "OE2" Residue "k PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 141": "OD1" <-> "OD2" Residue "l TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 8": "OD1" <-> "OD2" Residue "p PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 123": "OE1" <-> "OE2" Residue "p TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 67": "OE1" <-> "OE2" Residue "q TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 17.98, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 21.73 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 15.90 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: 21.51 Time building geometry restraints manager: 22.60 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: 97.43 - 105.22: 5103 105.22 - 113.01: 22693 113.01 - 120.80: 16538 120.80 - 128.59: 9716 128.59 - 136.38: 1552 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 2.440 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 2.520 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 ========== 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: 1.920 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: 0.020 Extract box with map and model: 8.830 Check model and map are aligned: 0.570 Set scattering table: 0.340 Process input model: 110.940 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.260 ------------------------------------------------------------------------------- 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= 0.217 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (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 TRP 0.010 0.001 TRP y 60 HIS 0.014 0.001 HIS q 117 PHE 0.024 0.002 PHE l 19 TYR 0.038 0.002 TYR A 75 ARG 0.005 0.001 ARG q 121 *********************** 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 fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.227 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: 0.4914 time to fit residues: 87.5261 Evaluate side-chains 79 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 30.0000 chunk 185 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 chunk 192 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 142 optimal weight: 30.0000 chunk 222 optimal weight: 9.9990 overall best weight: 14.9996 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 ASN ** n 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 37246 Z= 0.456 Angle : 0.973 10.633 55602 Z= 0.477 Chirality : 0.048 0.298 7076 Planarity : 0.007 0.074 3064 Dihedral : 27.292 179.005 18386 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 49.28 Ramachandran Plot: Outliers : 0.57 % Allowed : 9.74 % Favored : 89.69 % Rotamer: Outliers : 0.51 % Allowed : 6.91 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.21), residues: 1406 helix: -0.12 (0.22), residues: 509 sheet: -1.60 (0.35), residues: 207 loop : -1.99 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP y 60 HIS 0.009 0.003 HIS l 197 PHE 0.024 0.003 PHE n 80 TYR 0.058 0.003 TYR A 75 ARG 0.007 0.001 ARG 2 6 *********************** 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 97 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 1.639 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: 0.9466 (ppp) cc_final: 0.9250 (ppp) REVERT: l 19 PHE cc_start: 0.6455 (t80) cc_final: 0.6083 (t80) REVERT: n 61 LEU cc_start: 0.9194 (tt) cc_final: 0.8671 (tt) outliers start: 6 outliers final: 3 residues processed: 97 average time/residue: 0.4920 time to fit residues: 78.1529 Evaluate side-chains 79 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 185 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 240 optimal weight: 9.9990 chunk 198 optimal weight: 30.0000 chunk 221 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 overall best weight: 10.7992 ------------------------------------------------------------------------------- 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** P 50 ASN ** k 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 37246 Z= 0.329 Angle : 0.791 11.123 55602 Z= 0.395 Chirality : 0.042 0.300 7076 Planarity : 0.006 0.061 3064 Dihedral : 26.978 179.654 18386 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 36.93 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.04 % Favored : 91.54 % Rotamer: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.22), residues: 1406 helix: 0.25 (0.22), residues: 510 sheet: -1.69 (0.34), residues: 205 loop : -1.94 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP y 60 HIS 0.011 0.002 HIS t 76 PHE 0.021 0.002 PHE u 42 TYR 0.043 0.002 TYR A 75 ARG 0.007 0.001 ARG t 82 *********************** 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 86 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 2.067 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: 0.6816 (t80) cc_final: 0.6377 (t80) REVERT: n 59 TYR cc_start: 0.8946 (m-80) cc_final: 0.8545 (m-80) REVERT: p 95 MET cc_start: 0.9286 (tpt) cc_final: 0.9084 (tpp) REVERT: p 110 MET cc_start: 0.8871 (mpp) cc_final: 0.8484 (mpp) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.5198 time to fit residues: 72.1334 Evaluate side-chains 77 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 149 optimal weight: 0.9980 chunk 223 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 212 optimal weight: 0.4980 chunk 63 optimal weight: 20.0000 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 30 ASN ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37246 Z= 0.209 Angle : 0.674 9.755 55602 Z= 0.339 Chirality : 0.037 0.297 7076 Planarity : 0.005 0.057 3064 Dihedral : 26.607 176.735 18386 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 27.53 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.54 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1406 helix: 0.67 (0.23), residues: 510 sheet: -1.52 (0.35), residues: 195 loop : -1.88 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP y 60 HIS 0.008 0.001 HIS t 76 PHE 0.016 0.002 PHE n 80 TYR 0.034 0.002 TYR A 75 ARG 0.007 0.001 ARG q 12 *********************** 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 105 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.897 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: 3 53 MET cc_start: 0.9426 (ppp) cc_final: 0.9226 (ppp) REVERT: n 59 TYR cc_start: 0.8892 (m-80) cc_final: 0.8483 (m-80) REVERT: p 26 MET cc_start: 0.6957 (mpp) cc_final: 0.5242 (mpp) REVERT: p 110 MET cc_start: 0.8734 (mpp) cc_final: 0.8298 (mpp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.4938 time to fit residues: 83.5439 Evaluate side-chains 79 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 40.0000 chunk 134 optimal weight: 0.4980 chunk 3 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 97 optimal weight: 30.0000 chunk 202 optimal weight: 40.0000 chunk 163 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 120 optimal weight: 40.0000 chunk 212 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 overall best weight: 7.2990 ------------------------------------------------------------------------------- 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 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 37246 Z= 0.243 Angle : 0.692 10.346 55602 Z= 0.348 Chirality : 0.038 0.301 7076 Planarity : 0.005 0.060 3064 Dihedral : 26.619 174.288 18386 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 31.00 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.18 % Favored : 91.47 % Rotamer: Outliers : 0.08 % Allowed : 2.86 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.22), residues: 1406 helix: 0.71 (0.23), residues: 509 sheet: -1.60 (0.34), residues: 195 loop : -1.91 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP y 60 HIS 0.012 0.002 HIS t 76 PHE 0.013 0.002 PHE l 19 TYR 0.039 0.002 TYR A 75 ARG 0.005 0.000 ARG t 82 *********************** 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 88 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 2.071 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: 0.7913 (t80) cc_final: 0.7344 (t80) REVERT: n 59 TYR cc_start: 0.8932 (m-80) cc_final: 0.8536 (m-80) REVERT: p 110 MET cc_start: 0.8773 (mpp) cc_final: 0.8380 (mpp) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.5075 time to fit residues: 72.4091 Evaluate side-chains 76 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 237 optimal weight: 30.0000 chunk 196 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 overall best weight: 15.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 53 GLN 3 81 GLN ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 37246 Z= 0.456 Angle : 0.926 13.831 55602 Z= 0.458 Chirality : 0.048 0.312 7076 Planarity : 0.006 0.072 3064 Dihedral : 27.080 177.739 18386 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 50.61 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.31 % Favored : 88.34 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.21), residues: 1406 helix: -0.05 (0.22), residues: 508 sheet: -1.98 (0.33), residues: 191 loop : -2.06 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP y 60 HIS 0.028 0.003 HIS t 76 PHE 0.014 0.002 PHE A 98 TYR 0.056 0.003 TYR A 75 ARG 0.018 0.001 ARG n 24 *********************** 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 82 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.279 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: 0.8112 (t80) cc_final: 0.7452 (t80) REVERT: n 59 TYR cc_start: 0.8832 (m-80) cc_final: 0.8460 (m-80) REVERT: p 110 MET cc_start: 0.8569 (mpp) cc_final: 0.8195 (mpp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.5357 time to fit residues: 70.2949 Evaluate side-chains 71 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 173 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 199 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 236 optimal weight: 8.9990 chunk 147 optimal weight: 0.4980 chunk 143 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 overall best weight: 4.6586 ------------------------------------------------------------------------------- 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** ** p 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37246 Z= 0.189 Angle : 0.675 10.477 55602 Z= 0.340 Chirality : 0.037 0.315 7076 Planarity : 0.004 0.053 3064 Dihedral : 26.511 178.188 18386 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 26.30 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.47 % Favored : 93.17 % 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 : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.22), residues: 1406 helix: 0.62 (0.23), residues: 509 sheet: -1.69 (0.34), residues: 186 loop : -1.93 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP y 60 HIS 0.018 0.001 HIS t 76 PHE 0.010 0.001 PHE 3 30 TYR 0.035 0.002 TYR A 75 ARG 0.019 0.001 ARG A 14 *********************** 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 94 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 2.087 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: n 59 TYR cc_start: 0.8846 (m-80) cc_final: 0.8505 (m-80) REVERT: n 90 MET cc_start: 0.9255 (mmp) cc_final: 0.8998 (mmm) REVERT: p 110 MET cc_start: 0.8770 (mpp) cc_final: 0.8413 (mpp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.5072 time to fit residues: 76.3726 Evaluate side-chains 74 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 0.0370 chunk 94 optimal weight: 40.0000 chunk 141 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 45 optimal weight: 30.0000 chunk 150 optimal weight: 0.4980 chunk 160 optimal weight: 8.9990 chunk 116 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 overall best weight: 3.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 53 GLN ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37246 Z= 0.164 Angle : 0.624 9.979 55602 Z= 0.318 Chirality : 0.035 0.280 7076 Planarity : 0.004 0.054 3064 Dihedral : 26.211 177.143 18386 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 24.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.68 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.22), residues: 1406 helix: 0.96 (0.23), residues: 506 sheet: -1.45 (0.35), residues: 188 loop : -1.86 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP n 42 HIS 0.017 0.001 HIS t 76 PHE 0.009 0.001 PHE 3 30 TYR 0.035 0.001 TYR A 75 ARG 0.010 0.000 ARG n 24 *********************** 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 103 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.987 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: 0.8164 (t80) cc_final: 0.7486 (t80) REVERT: n 59 TYR cc_start: 0.9021 (m-80) cc_final: 0.8699 (m-80) REVERT: n 62 MET cc_start: 0.9520 (tpt) cc_final: 0.9294 (tpt) REVERT: n 88 MET cc_start: 0.8324 (tmm) cc_final: 0.8052 (tmm) REVERT: n 90 MET cc_start: 0.9202 (mmp) cc_final: 0.8999 (mmp) REVERT: p 110 MET cc_start: 0.8757 (mpp) cc_final: 0.8399 (mpp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.4734 time to fit residues: 79.5808 Evaluate side-chains 78 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 9.9990 chunk 226 optimal weight: 0.3980 chunk 206 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 132 optimal weight: 30.0000 chunk 95 optimal weight: 20.0000 chunk 172 optimal weight: 50.0000 chunk 67 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 53 GLN ** P 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 17 GLN ** p 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37246 Z= 0.189 Angle : 0.634 10.146 55602 Z= 0.321 Chirality : 0.036 0.285 7076 Planarity : 0.004 0.053 3064 Dihedral : 26.239 179.463 18386 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 25.89 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.33 % Favored : 92.39 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.22), residues: 1406 helix: 0.96 (0.24), residues: 506 sheet: -1.44 (0.35), residues: 183 loop : -1.83 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP y 60 HIS 0.016 0.001 HIS t 76 PHE 0.019 0.001 PHE 3 30 TYR 0.037 0.002 TYR A 75 ARG 0.008 0.000 ARG n 38 *********************** 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 95 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 2.276 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: l 19 PHE cc_start: 0.8218 (t80) cc_final: 0.7560 (t80) REVERT: n 59 TYR cc_start: 0.8933 (m-80) cc_final: 0.8597 (m-80) REVERT: n 62 MET cc_start: 0.9489 (tpt) cc_final: 0.9288 (tpt) REVERT: n 88 MET cc_start: 0.8167 (tmm) cc_final: 0.7824 (tmm) REVERT: p 110 MET cc_start: 0.8583 (mpp) cc_final: 0.8251 (mpp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.4738 time to fit residues: 74.2935 Evaluate side-chains 68 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 9.9990 chunk 232 optimal weight: 7.9990 chunk 142 optimal weight: 0.2980 chunk 110 optimal weight: 20.0000 chunk 161 optimal weight: 0.5980 chunk 244 optimal weight: 0.6980 chunk 224 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 119 optimal weight: 30.0000 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 53 GLN P 30 HIS ** k 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 37246 Z= 0.145 Angle : 0.600 10.963 55602 Z= 0.305 Chirality : 0.034 0.275 7076 Planarity : 0.004 0.048 3064 Dihedral : 25.999 178.558 18386 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.69 % Favored : 93.03 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1406 helix: 1.00 (0.24), residues: 509 sheet: -1.29 (0.36), residues: 182 loop : -1.82 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP l 169 HIS 0.015 0.001 HIS t 76 PHE 0.024 0.001 PHE l 19 TYR 0.032 0.001 TYR A 75 ARG 0.007 0.000 ARG n 24 ********************** 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 99 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.281 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 110 MET cc_start: 0.8304 (tmm) cc_final: 0.8034 (tmm) REVERT: l 19 PHE cc_start: 0.8074 (t80) cc_final: 0.7833 (t80) REVERT: n 62 MET cc_start: 0.9500 (tpt) cc_final: 0.9204 (tpt) REVERT: n 88 MET cc_start: 0.8312 (tmm) cc_final: 0.8103 (tmm) REVERT: p 110 MET cc_start: 0.8578 (mpp) cc_final: 0.8228 (mpp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.4736 time to fit residues: 78.0540 Evaluate side-chains 77 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 194 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 199 optimal weight: 50.0000 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 overall best weight: 11.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 53 GLN ** k 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 14 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 = 0.024377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.016152 restraints weight = 700874.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.016665 restraints weight = 299393.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.016876 restraints weight = 196835.174| |-----------------------------------------------------------------------------| r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 37246 Z= 0.371 Angle : 0.817 10.841 55602 Z= 0.406 Chirality : 0.043 0.293 7076 Planarity : 0.006 0.066 3064 Dihedral : 26.641 176.279 18386 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 40.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.17 % Favored : 89.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1406 helix: 0.42 (0.23), residues: 508 sheet: -1.68 (0.35), residues: 182 loop : -1.92 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP q 43 HIS 0.018 0.002 HIS t 76 PHE 0.024 0.002 PHE l 19 TYR 0.058 0.003 TYR A 75 ARG 0.009 0.001 ARG n 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4151.15 seconds wall clock time: 79 minutes 15.26 seconds (4755.26 seconds total)