Starting phenix.real_space_refine on Tue Nov 19 12:08:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/11_2024/6gc7_4382.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/11_2024/6gc7_4382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/11_2024/6gc7_4382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/11_2024/6gc7_4382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/11_2024/6gc7_4382.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/11_2024/6gc7_4382.cif" } resolution = 4.3 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= 0.070 sd= 0.500 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 1901 5.49 5 S 39 5.16 5 C 26713 2.51 5 N 10181 2.21 5 O 15576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 54410 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 40850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1901, 40850 Classifications: {'RNA': 1901} Modifications used: {'rna2p_pur': 182, 'rna2p_pyr': 102, 'rna3p_pur': 933, 'rna3p_pyr': 684} Link IDs: {'rna2p': 284, 'rna3p': 1616} Chain breaks: 8 Chain: "D" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1366 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 1 Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 778 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain breaks: 1 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Time building chain proxies: 29.26, per 1000 atoms: 0.54 Number of scatterers: 54410 At special positions: 0 Unit cell: (210.8, 163.68, 210.8, 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 39 16.00 P 1901 15.00 O 15576 8.00 N 10181 7.00 C 26713 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: 12.37 Conformation dependent library (CDL) restraints added in 2.5 seconds 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 24 sheets defined 30.0% alpha, 19.9% beta 525 base pairs and 981 stacking pairs defined. Time for finding SS restraints: 24.84 Creating SS restraints... Processing helix chain 'D' and resid 61 through 66 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 37 removed outlier: 3.645A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 113 removed outlier: 3.844A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.574A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 4.078A pdb=" N ILE E 175 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 201 removed outlier: 3.778A pdb=" N GLN E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU E 197 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.719A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY J 38 " --> pdb=" O ARG J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.671A pdb=" N LYS J 61 " --> pdb=" O ASN J 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL J 62 " --> pdb=" O ALA J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 58 through 62' Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.094A pdb=" N LYS J 72 " --> pdb=" O LYS J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 removed outlier: 3.557A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 108 removed outlier: 4.175A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.929A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.547A pdb=" N GLN J 135 " --> pdb=" O HIS J 132 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 132 through 136' Processing helix chain 'K' and resid 114 through 118 removed outlier: 3.801A pdb=" N SER K 117 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 26 removed outlier: 3.883A pdb=" N SER L 25 " --> pdb=" O GLY L 22 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY L 26 " --> pdb=" O ILE L 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 22 through 26' Processing helix chain 'L' and resid 29 through 33 removed outlier: 3.623A pdb=" N GLY L 32 " --> pdb=" O LYS L 29 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG L 33 " --> pdb=" O THR L 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 29 through 33' Processing helix chain 'L' and resid 130 through 135 removed outlier: 4.215A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE L 135 " --> pdb=" O ALA L 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 130 through 135' Processing helix chain 'L' and resid 136 through 139 removed outlier: 3.724A pdb=" N GLY L 139 " --> pdb=" O GLU L 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 136 through 139' Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.641A pdb=" N ARG N 17 " --> pdb=" O ASN N 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 55 removed outlier: 3.508A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 61 through 69 removed outlier: 3.650A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 78 removed outlier: 3.668A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 removed outlier: 3.562A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 10 removed outlier: 3.544A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 removed outlier: 3.707A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU P 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 18 removed outlier: 4.207A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 28 removed outlier: 3.979A pdb=" N ARG Q 27 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 69 removed outlier: 3.981A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.657A pdb=" N LEU Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 115 removed outlier: 3.686A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 22 removed outlier: 3.744A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.735A pdb=" N LEU S 33 " --> pdb=" O VAL S 29 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 61 removed outlier: 3.891A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 3 through 9 removed outlier: 4.137A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.691A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'Y' and resid 2 through 7 Processing helix chain 'Y' and resid 9 through 23 removed outlier: 3.575A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 30 removed outlier: 3.528A pdb=" N MET Y 30 " --> pdb=" O PHE Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 44 removed outlier: 4.328A pdb=" N LEU Y 42 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 56 Processing helix chain '0' and resid 8 through 16 Processing helix chain '0' and resid 17 through 20 removed outlier: 4.176A pdb=" N ALA 0 20 " --> pdb=" O SER 0 17 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 17 through 20' Processing helix chain '2' and resid 8 through 16 removed outlier: 3.572A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 26 through 38 Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.856A pdb=" N THR Z 22 " --> pdb=" O LYS Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 48 Processing sheet with id=AA1, first strand: chain 'D' and resid 21 through 28 removed outlier: 6.664A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.235A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG D 33 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 120 removed outlier: 3.992A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG E 170 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 122 through 124 removed outlier: 3.589A pdb=" N LEU J 57 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN J 138 " --> pdb=" O TRP J 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 73 through 76 Processing sheet with id=AA7, first strand: chain 'K' and resid 6 through 10 removed outlier: 4.068A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ARG K 17 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA K 46 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL K 19 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS K 44 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N CYS K 21 " --> pdb=" O THR K 42 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR K 42 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL K 63 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 69 through 70 removed outlier: 4.719A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG P 71 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL P 60 " --> pdb=" O ARG P 71 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 69 through 70 removed outlier: 4.719A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG P 71 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL P 60 " --> pdb=" O ARG P 71 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 121 through 122 Processing sheet with id=AB2, first strand: chain 'N' and resid 33 through 36 removed outlier: 3.548A pdb=" N GLU N 114 " --> pdb=" O ARG N 96 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 2 through 6 Processing sheet with id=AB4, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.842A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.219A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 3 through 8 removed outlier: 3.680A pdb=" N PHE S 75 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 82 through 87 removed outlier: 3.601A pdb=" N ARG S 84 " --> pdb=" O ILE S 96 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP S 94 " --> pdb=" O MET S 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'T' and resid 13 through 14 removed outlier: 3.744A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP T 80 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'T' and resid 67 through 68 Processing sheet with id=AC1, first strand: chain 'U' and resid 63 through 65 removed outlier: 3.519A pdb=" N ILE U 11 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA U 70 " --> pdb=" O ILE U 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 40 through 41 removed outlier: 3.565A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 83 through 86 removed outlier: 3.624A pdb=" N GLY U 83 " --> pdb=" O PHE U 94 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE U 94 " --> pdb=" O GLY U 83 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG U 85 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AC5, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AC6, first strand: chain 'Z' and resid 34 through 37 removed outlier: 3.956A pdb=" N ARG Z 37 " --> pdb=" O ILE Z 4 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE Z 4 " --> pdb=" O ARG Z 37 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1324 hydrogen bonds 2100 hydrogen bond angles 0 basepair planarities 525 basepair parallelities 981 stacking parallelities Total time for adding SS restraints: 61.21 Time building geometry restraints manager: 14.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7772 1.33 - 1.45: 25398 1.45 - 1.57: 22433 1.57 - 1.69: 3795 1.69 - 1.81: 75 Bond restraints: 59473 Sorted by residual: bond pdb=" CA ASN U 98 " pdb=" CB ASN U 98 " ideal model delta sigma weight residual 1.532 1.571 -0.040 1.33e-02 5.65e+03 8.87e+00 bond pdb=" CB ASN U 98 " pdb=" CG ASN U 98 " ideal model delta sigma weight residual 1.516 1.573 -0.057 2.50e-02 1.60e+03 5.29e+00 bond pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 4.10e+00 bond pdb=" C3' G A 271 " pdb=" O3' G A 271 " ideal model delta sigma weight residual 1.427 1.455 -0.028 1.50e-02 4.44e+03 3.61e+00 bond pdb=" C ALA K 119 " pdb=" N PRO K 120 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.19e-02 7.06e+03 3.36e+00 ... (remaining 59468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 88601 2.42 - 4.85: 1009 4.85 - 7.27: 109 7.27 - 9.70: 18 9.70 - 12.12: 5 Bond angle restraints: 89742 Sorted by residual: angle pdb=" C ILE T 2 " pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 121.70 133.66 -11.96 1.80e+00 3.09e-01 4.41e+01 angle pdb=" C GLN Y 45 " pdb=" N VAL Y 46 " pdb=" CA VAL Y 46 " ideal model delta sigma weight residual 121.97 132.94 -10.97 1.80e+00 3.09e-01 3.71e+01 angle pdb=" C VAL 0 53 " pdb=" N ILE 0 54 " pdb=" CA ILE 0 54 " ideal model delta sigma weight residual 120.77 127.94 -7.17 1.31e+00 5.83e-01 2.99e+01 angle pdb=" C GLY L 114 " pdb=" N GLU L 115 " pdb=" CA GLU L 115 " ideal model delta sigma weight residual 122.46 129.91 -7.45 1.41e+00 5.03e-01 2.79e+01 angle pdb=" C SER U 97 " pdb=" N ASN U 98 " pdb=" CA ASN U 98 " ideal model delta sigma weight residual 124.82 133.74 -8.92 1.78e+00 3.16e-01 2.51e+01 ... (remaining 89737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 33348 35.16 - 70.32: 4195 70.32 - 105.48: 497 105.48 - 140.64: 2 140.64 - 175.80: 7 Dihedral angle restraints: 38049 sinusoidal: 33111 harmonic: 4938 Sorted by residual: dihedral pdb=" O4' U A1174 " pdb=" C1' U A1174 " pdb=" N1 U A1174 " pdb=" C2 U A1174 " ideal model delta sinusoidal sigma weight residual 200.00 43.94 156.06 1 1.50e+01 4.44e-03 8.17e+01 dihedral pdb=" O4' U A 646 " pdb=" C1' U A 646 " pdb=" N1 U A 646 " pdb=" C2 U A 646 " ideal model delta sinusoidal sigma weight residual 200.00 44.19 155.81 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 64.26 135.74 1 1.50e+01 4.44e-03 7.32e+01 ... (remaining 38046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 11102 0.070 - 0.141: 454 0.141 - 0.211: 41 0.211 - 0.281: 3 0.281 - 0.352: 3 Chirality restraints: 11603 Sorted by residual: chirality pdb=" CB VAL L 110 " pdb=" CA VAL L 110 " pdb=" CG1 VAL L 110 " pdb=" CG2 VAL L 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C3' A A1378 " pdb=" C4' A A1378 " pdb=" O3' A A1378 " pdb=" C2' A A1378 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' G A 271 " pdb=" C4' G A 271 " pdb=" O3' G A 271 " pdb=" C2' G A 271 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 11600 not shown) Planarity restraints: 4258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 635 " 0.006 2.00e-02 2.50e+03 1.75e-02 6.90e+00 pdb=" N1 C A 635 " -0.003 2.00e-02 2.50e+03 pdb=" C2 C A 635 " 0.040 2.00e-02 2.50e+03 pdb=" O2 C A 635 " -0.031 2.00e-02 2.50e+03 pdb=" N3 C A 635 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C A 635 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C A 635 " -0.001 2.00e-02 2.50e+03 pdb=" C5 C A 635 " -0.007 2.00e-02 2.50e+03 pdb=" C6 C A 635 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR Z 40 " 0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO Z 41 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO Z 41 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO Z 41 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U A1736 " -0.028 2.00e-02 2.50e+03 1.64e-02 6.02e+00 pdb=" N1 U A1736 " 0.037 2.00e-02 2.50e+03 pdb=" C2 U A1736 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U A1736 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U A1736 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U A1736 " -0.013 2.00e-02 2.50e+03 pdb=" O4 U A1736 " -0.000 2.00e-02 2.50e+03 pdb=" C5 U A1736 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U A1736 " 0.006 2.00e-02 2.50e+03 ... (remaining 4255 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 10727 2.78 - 3.31: 43025 3.31 - 3.84: 113797 3.84 - 4.37: 130828 4.37 - 4.90: 174227 Nonbonded interactions: 472604 Sorted by model distance: nonbonded pdb=" O2 C A 269 " pdb=" N2 G A 370 " model vdw 2.251 2.496 nonbonded pdb=" O2 C A 335 " pdb=" OG SER U 67 " model vdw 2.261 3.040 nonbonded pdb=" O2' U A 571 " pdb=" OP2 U A 573 " model vdw 2.268 3.040 nonbonded pdb=" O ILE S 35 " pdb=" OG1 THR S 39 " model vdw 2.281 3.040 nonbonded pdb=" O2' C A 239 " pdb=" O2' G A 622 " model vdw 2.284 3.040 ... (remaining 472599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.050 Extract box with map and model: 1.970 Check model and map are aligned: 0.380 Set scattering table: 0.470 Process input model: 159.060 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 59473 Z= 0.158 Angle : 0.671 12.122 89742 Z= 0.346 Chirality : 0.031 0.352 11603 Planarity : 0.004 0.063 4258 Dihedral : 22.572 175.805 34857 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.95 % Rotamer: Outliers : 0.28 % Allowed : 3.60 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.27 (0.15), residues: 1702 helix: -4.15 (0.12), residues: 445 sheet: -1.63 (0.28), residues: 303 loop : -2.61 (0.15), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Q 60 HIS 0.004 0.001 HIS R 82 PHE 0.019 0.002 PHE Q 35 TYR 0.016 0.002 TYR Q 44 ARG 0.011 0.001 ARG 2 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 788 time to evaluate : 3.070 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 ASP cc_start: 0.5858 (m-30) cc_final: 0.5245 (m-30) REVERT: D 90 PHE cc_start: 0.6067 (m-80) cc_final: 0.5654 (m-80) REVERT: J 10 THR cc_start: 0.6238 (p) cc_final: 0.5986 (p) REVERT: J 100 VAL cc_start: 0.8461 (t) cc_final: 0.8126 (p) REVERT: J 124 VAL cc_start: 0.8805 (p) cc_final: 0.8602 (p) REVERT: K 73 ASP cc_start: 0.6205 (p0) cc_final: 0.5983 (p0) REVERT: K 97 THR cc_start: 0.7551 (p) cc_final: 0.7346 (p) REVERT: N 10 LEU cc_start: 0.7746 (mt) cc_final: 0.7509 (mp) REVERT: P 30 TRP cc_start: 0.6142 (m100) cc_final: 0.5647 (m100) REVERT: Q 8 ILE cc_start: 0.8036 (pp) cc_final: 0.7519 (mm) REVERT: Q 59 LEU cc_start: 0.6698 (tp) cc_final: 0.6110 (tt) REVERT: Q 80 ASN cc_start: 0.7036 (t0) cc_final: 0.6766 (t0) REVERT: Q 116 LEU cc_start: 0.6921 (tt) cc_final: 0.6430 (tt) REVERT: S 51 LEU cc_start: 0.6897 (tp) cc_final: 0.6522 (tp) REVERT: Y 22 LEU cc_start: 0.7652 (tp) cc_final: 0.7181 (tt) REVERT: 2 31 LEU cc_start: 0.7847 (mt) cc_final: 0.6749 (mm) REVERT: Z 15 ARG cc_start: 0.7151 (tpp-160) cc_final: 0.6901 (tpp-160) outliers start: 4 outliers final: 1 residues processed: 789 average time/residue: 0.7965 time to fit residues: 975.6599 Evaluate side-chains 444 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 443 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 8.9990 chunk 271 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 280 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 208 optimal weight: 0.4980 chunk 325 optimal weight: 9.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN E 115 GLN J 76 HIS J 132 HIS N 11 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN P 74 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN Q 55 GLN R 6 GLN R 86 GLN S 7 HIS T 15 HIS U 44 HIS Y 25 GLN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 59473 Z= 0.326 Angle : 0.722 15.807 89742 Z= 0.370 Chirality : 0.037 0.317 11603 Planarity : 0.006 0.175 4258 Dihedral : 23.682 179.223 31454 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.82 % Favored : 93.01 % Rotamer: Outliers : 0.14 % Allowed : 4.94 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.72 (0.18), residues: 1702 helix: -1.69 (0.21), residues: 467 sheet: -1.25 (0.28), residues: 318 loop : -2.07 (0.18), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP Q 60 HIS 0.009 0.002 HIS P 55 PHE 0.021 0.003 PHE U 94 TYR 0.016 0.002 TYR J 75 ARG 0.024 0.001 ARG K 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 563 time to evaluate : 2.884 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 PHE cc_start: 0.7259 (m-80) cc_final: 0.6117 (m-80) REVERT: D 79 LEU cc_start: 0.7775 (mm) cc_final: 0.7540 (mm) REVERT: D 103 ASP cc_start: 0.6186 (p0) cc_final: 0.5896 (p0) REVERT: E 106 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8163 (mttt) REVERT: E 108 ILE cc_start: 0.7698 (pt) cc_final: 0.7361 (pt) REVERT: J 16 TYR cc_start: 0.7859 (m-80) cc_final: 0.7591 (m-80) REVERT: J 49 ASP cc_start: 0.6009 (t0) cc_final: 0.5308 (t0) REVERT: J 74 TYR cc_start: 0.6747 (m-80) cc_final: 0.6532 (m-80) REVERT: J 78 THR cc_start: 0.3947 (p) cc_final: 0.3207 (p) REVERT: K 1 MET cc_start: 0.6402 (pmm) cc_final: 0.6059 (pmm) REVERT: K 67 LYS cc_start: 0.6275 (tptt) cc_final: 0.5965 (tppp) REVERT: K 73 ASP cc_start: 0.7338 (p0) cc_final: 0.6712 (p0) REVERT: L 29 LYS cc_start: 0.5454 (mtpt) cc_final: 0.5144 (mtmt) REVERT: P 15 ASP cc_start: 0.7236 (p0) cc_final: 0.6533 (t0) REVERT: P 55 HIS cc_start: 0.7135 (m170) cc_final: 0.6932 (m170) REVERT: P 73 PHE cc_start: 0.7147 (m-80) cc_final: 0.6284 (m-10) REVERT: R 32 THR cc_start: 0.7638 (m) cc_final: 0.7399 (p) REVERT: R 71 LYS cc_start: 0.8336 (tptt) cc_final: 0.8095 (tttt) REVERT: R 76 LYS cc_start: 0.7265 (mttt) cc_final: 0.6801 (mttm) REVERT: R 91 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8232 (tp-100) REVERT: S 66 ILE cc_start: 0.7988 (pt) cc_final: 0.7532 (pt) REVERT: S 68 ASP cc_start: 0.6926 (m-30) cc_final: 0.6723 (m-30) REVERT: S 99 ARG cc_start: 0.7480 (mmt90) cc_final: 0.7220 (mpt-90) REVERT: T 22 THR cc_start: 0.8706 (p) cc_final: 0.8404 (t) REVERT: Z 15 ARG cc_start: 0.6999 (tpp-160) cc_final: 0.6203 (tpp-160) outliers start: 2 outliers final: 1 residues processed: 564 average time/residue: 0.7630 time to fit residues: 684.7233 Evaluate side-chains 421 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 420 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 180 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 270 optimal weight: 0.8980 chunk 221 optimal weight: 10.0000 chunk 89 optimal weight: 30.0000 chunk 325 optimal weight: 10.0000 chunk 351 optimal weight: 9.9990 chunk 290 optimal weight: 0.9980 chunk 322 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 overall best weight: 5.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 HIS J 58 ASN J 80 HIS J 132 HIS K 5 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN Q 55 GLN ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 82 HIS U 53 GLN Y 25 GLN 0 18 HIS Z 19 HIS ** Z 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 59473 Z= 0.288 Angle : 0.638 11.837 89742 Z= 0.330 Chirality : 0.035 0.264 11603 Planarity : 0.006 0.109 4258 Dihedral : 23.763 173.620 31454 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.58 % Favored : 93.30 % Rotamer: Outliers : 0.14 % Allowed : 4.65 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.25 (0.19), residues: 1702 helix: -1.19 (0.22), residues: 482 sheet: -0.90 (0.27), residues: 333 loop : -1.89 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Q 60 HIS 0.008 0.002 HIS P 55 PHE 0.027 0.003 PHE P 73 TYR 0.029 0.002 TYR Q 44 ARG 0.019 0.001 ARG K 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 526 time to evaluate : 2.926 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: 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: symmetry clash revert: symmetry clash REVERT: D 15 PHE cc_start: 0.7302 (m-80) cc_final: 0.6701 (m-80) REVERT: D 43 ASP cc_start: 0.7165 (m-30) cc_final: 0.6387 (m-30) REVERT: J 32 LEU cc_start: 0.8494 (pp) cc_final: 0.8257 (pp) REVERT: J 78 THR cc_start: 0.4591 (p) cc_final: 0.4354 (p) REVERT: K 1 MET cc_start: 0.6489 (pmm) cc_final: 0.5683 (pmm) REVERT: K 63 VAL cc_start: 0.7116 (m) cc_final: 0.6736 (p) REVERT: K 73 ASP cc_start: 0.7502 (p0) cc_final: 0.6882 (p0) REVERT: P 15 ASP cc_start: 0.6925 (p0) cc_final: 0.6535 (t0) REVERT: Q 44 TYR cc_start: 0.7359 (m-80) cc_final: 0.7119 (m-10) REVERT: Q 93 ILE cc_start: 0.7443 (mm) cc_final: 0.6971 (mm) REVERT: R 98 ILE cc_start: 0.6827 (tp) cc_final: 0.6583 (tt) REVERT: S 12 SER cc_start: 0.7533 (p) cc_final: 0.7292 (p) REVERT: S 22 ASP cc_start: 0.6950 (p0) cc_final: 0.6620 (p0) REVERT: S 38 TYR cc_start: 0.6297 (m-80) cc_final: 0.5848 (m-10) REVERT: T 22 THR cc_start: 0.8639 (p) cc_final: 0.8305 (t) REVERT: T 50 LEU cc_start: 0.7285 (mm) cc_final: 0.7057 (mm) REVERT: 0 36 LYS cc_start: 0.7492 (ptpt) cc_final: 0.7225 (pttt) outliers start: 2 outliers final: 0 residues processed: 528 average time/residue: 0.7467 time to fit residues: 632.8830 Evaluate side-chains 403 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 321 optimal weight: 0.0000 chunk 244 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 36 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 326 optimal weight: 10.0000 chunk 346 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 309 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 overall best weight: 4.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 58 ASN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS K 3 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN P 76 HIS Q 55 GLN Q 70 GLN R 6 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS U 44 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN Y 25 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 13 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 59473 Z= 0.254 Angle : 0.611 16.248 89742 Z= 0.316 Chirality : 0.034 0.270 11603 Planarity : 0.005 0.111 4258 Dihedral : 23.766 172.696 31454 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.64 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.07 (0.19), residues: 1702 helix: -0.88 (0.23), residues: 496 sheet: -0.77 (0.29), residues: 301 loop : -1.89 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP Q 60 HIS 0.007 0.001 HIS U 44 PHE 0.023 0.002 PHE P 73 TYR 0.017 0.002 TYR Q 44 ARG 0.009 0.001 ARG 2 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 2.900 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: 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: D 18 ASP cc_start: 0.6063 (p0) cc_final: 0.5824 (p0) REVERT: D 43 ASP cc_start: 0.7231 (m-30) cc_final: 0.6401 (m-30) REVERT: J 57 LEU cc_start: 0.7619 (tp) cc_final: 0.7415 (tp) REVERT: J 100 VAL cc_start: 0.8602 (t) cc_final: 0.8356 (p) REVERT: K 1 MET cc_start: 0.6780 (pmm) cc_final: 0.6399 (pmm) REVERT: K 73 ASP cc_start: 0.7169 (p0) cc_final: 0.6662 (p0) REVERT: P 12 MET cc_start: 0.6293 (mmt) cc_final: 0.5797 (mmt) REVERT: P 73 PHE cc_start: 0.6391 (m-10) cc_final: 0.6043 (m-10) REVERT: Q 92 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7725 (mmmt) REVERT: R 39 LEU cc_start: 0.8186 (mp) cc_final: 0.6487 (mt) REVERT: R 49 ILE cc_start: 0.4451 (pt) cc_final: 0.4187 (pt) REVERT: S 22 ASP cc_start: 0.6576 (p0) cc_final: 0.6361 (p0) REVERT: S 50 VAL cc_start: 0.7841 (t) cc_final: 0.7629 (t) REVERT: S 51 LEU cc_start: 0.6928 (tp) cc_final: 0.6699 (tp) REVERT: T 22 THR cc_start: 0.8683 (p) cc_final: 0.8463 (t) REVERT: T 25 GLU cc_start: 0.8307 (pt0) cc_final: 0.8052 (pt0) REVERT: 2 1 MET cc_start: 0.0855 (ppp) cc_final: 0.0492 (ttt) outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.7339 time to fit residues: 600.7306 Evaluate side-chains 396 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 288 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 257 optimal weight: 0.6980 chunk 142 optimal weight: 10.0000 chunk 295 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 310 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 132 HIS N 3 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN Q 70 GLN R 6 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 59473 Z= 0.161 Angle : 0.533 11.883 89742 Z= 0.275 Chirality : 0.031 0.261 11603 Planarity : 0.004 0.058 4258 Dihedral : 23.648 172.765 31454 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.23 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.82 (0.19), residues: 1702 helix: -0.61 (0.23), residues: 485 sheet: -0.67 (0.30), residues: 292 loop : -1.73 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP T 80 HIS 0.006 0.001 HIS U 44 PHE 0.019 0.002 PHE Y 26 TYR 0.012 0.002 TYR Q 75 ARG 0.009 0.001 ARG Z 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 519 time to evaluate : 2.800 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: 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: symmetry clash revert: symmetry clash REVERT: D 43 ASP cc_start: 0.7288 (m-30) cc_final: 0.6531 (m-30) REVERT: D 165 MET cc_start: 0.6830 (tmm) cc_final: 0.6624 (tmm) REVERT: J 114 LEU cc_start: 0.7688 (tp) cc_final: 0.7416 (tp) REVERT: K 63 VAL cc_start: 0.6960 (m) cc_final: 0.6743 (p) REVERT: K 67 LYS cc_start: 0.6719 (tptt) cc_final: 0.6288 (tppp) REVERT: K 73 ASP cc_start: 0.6934 (p0) cc_final: 0.6436 (p0) REVERT: N 20 MET cc_start: 0.5783 (tpp) cc_final: 0.5560 (tpt) REVERT: P 12 MET cc_start: 0.6293 (mmt) cc_final: 0.5811 (mmt) REVERT: R 49 ILE cc_start: 0.3884 (pt) cc_final: 0.3683 (pt) REVERT: R 76 LYS cc_start: 0.7317 (mttt) cc_final: 0.6957 (mttm) REVERT: S 23 LEU cc_start: 0.8622 (mt) cc_final: 0.8272 (mt) REVERT: T 22 THR cc_start: 0.8648 (p) cc_final: 0.8439 (t) REVERT: Y 8 GLU cc_start: 0.6492 (tm-30) cc_final: 0.6263 (tm-30) REVERT: 0 36 LYS cc_start: 0.7426 (mmmm) cc_final: 0.7082 (mtpp) REVERT: Z 26 LEU cc_start: 0.6681 (mm) cc_final: 0.6397 (mm) outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 0.7089 time to fit residues: 596.9434 Evaluate side-chains 416 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 116 optimal weight: 10.0000 chunk 311 optimal weight: 0.1980 chunk 68 optimal weight: 20.0000 chunk 203 optimal weight: 30.0000 chunk 85 optimal weight: 10.0000 chunk 346 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 160 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 114 optimal weight: 30.0000 chunk 181 optimal weight: 10.0000 overall best weight: 7.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS K 5 GLN K 9 ASN K 13 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN Y 25 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.7175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 59473 Z= 0.358 Angle : 0.732 11.434 89742 Z= 0.376 Chirality : 0.040 0.283 11603 Planarity : 0.006 0.060 4258 Dihedral : 24.033 167.439 31454 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.40 % Favored : 91.54 % Rotamer: Outliers : 0.07 % Allowed : 3.17 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.27 (0.18), residues: 1702 helix: -0.85 (0.22), residues: 477 sheet: -1.39 (0.26), residues: 333 loop : -1.91 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP T 80 HIS 0.008 0.002 HIS U 44 PHE 0.020 0.003 PHE Y 26 TYR 0.021 0.002 TYR S 38 ARG 0.012 0.001 ARG J 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 479 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 118 PHE cc_start: 0.6956 (t80) cc_final: 0.6689 (t80) REVERT: E 193 VAL cc_start: 0.7895 (m) cc_final: 0.7688 (p) REVERT: J 32 LEU cc_start: 0.8566 (pp) cc_final: 0.8224 (pp) REVERT: J 136 GLN cc_start: 0.8780 (mt0) cc_final: 0.8518 (mp10) REVERT: K 1 MET cc_start: 0.6368 (pmm) cc_final: 0.6037 (pmm) REVERT: K 67 LYS cc_start: 0.6790 (tptt) cc_final: 0.6160 (tppp) REVERT: K 73 ASP cc_start: 0.7080 (p0) cc_final: 0.6222 (p0) REVERT: P 26 GLU cc_start: 0.5381 (mp0) cc_final: 0.5153 (mp0) REVERT: P 105 LYS cc_start: 0.7633 (pttm) cc_final: 0.7428 (pttt) REVERT: R 76 LYS cc_start: 0.7353 (mttt) cc_final: 0.7138 (mttm) REVERT: S 22 ASP cc_start: 0.6885 (p0) cc_final: 0.6655 (p0) REVERT: S 51 LEU cc_start: 0.6895 (tp) cc_final: 0.6507 (tp) REVERT: T 22 THR cc_start: 0.8710 (p) cc_final: 0.8507 (t) REVERT: U 11 ILE cc_start: 0.6397 (mt) cc_final: 0.6171 (mt) REVERT: 0 36 LYS cc_start: 0.7715 (mmmm) cc_final: 0.7420 (mttm) REVERT: 2 1 MET cc_start: 0.0588 (ttt) cc_final: 0.0146 (ppp) outliers start: 1 outliers final: 1 residues processed: 479 average time/residue: 0.7310 time to fit residues: 570.2230 Evaluate side-chains 383 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 382 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 333 optimal weight: 0.5980 chunk 39 optimal weight: 40.0000 chunk 197 optimal weight: 7.9990 chunk 252 optimal weight: 7.9990 chunk 195 optimal weight: 20.0000 chunk 291 optimal weight: 0.9980 chunk 193 optimal weight: 10.0000 chunk 345 optimal weight: 9.9990 chunk 215 optimal weight: 0.5980 chunk 210 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 overall best weight: 3.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 132 HIS K 13 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 GLN R 6 GLN ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN 0 18 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.7147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 59473 Z= 0.206 Angle : 0.589 12.341 89742 Z= 0.305 Chirality : 0.033 0.325 11603 Planarity : 0.005 0.052 4258 Dihedral : 23.843 168.442 31454 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.29 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.03 (0.19), residues: 1702 helix: -0.72 (0.23), residues: 484 sheet: -1.17 (0.27), residues: 325 loop : -1.75 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 78 HIS 0.006 0.001 HIS 0 41 PHE 0.032 0.002 PHE D 15 TYR 0.020 0.002 TYR K 32 ARG 0.011 0.001 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 3.192 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 193 VAL cc_start: 0.7624 (m) cc_final: 0.7149 (p) REVERT: J 109 LEU cc_start: 0.8343 (mm) cc_final: 0.8137 (mm) REVERT: J 120 ARG cc_start: 0.7920 (mtt180) cc_final: 0.7386 (mmt180) REVERT: J 136 GLN cc_start: 0.8724 (mt0) cc_final: 0.7865 (mp10) REVERT: K 1 MET cc_start: 0.6180 (pmm) cc_final: 0.5976 (pmm) REVERT: K 67 LYS cc_start: 0.6600 (tptt) cc_final: 0.6123 (tppp) REVERT: K 73 ASP cc_start: 0.7053 (p0) cc_final: 0.6266 (p0) REVERT: K 107 LEU cc_start: 0.5282 (mp) cc_final: 0.4998 (mp) REVERT: N 35 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7774 (tttp) REVERT: P 12 MET cc_start: 0.6210 (mmt) cc_final: 0.5555 (mmt) REVERT: P 84 SER cc_start: 0.6375 (p) cc_final: 0.5633 (p) REVERT: R 76 LYS cc_start: 0.7270 (mttt) cc_final: 0.7061 (mttm) REVERT: R 98 ILE cc_start: 0.6185 (tt) cc_final: 0.5840 (tt) REVERT: S 51 LEU cc_start: 0.6841 (tp) cc_final: 0.6631 (tp) REVERT: T 22 THR cc_start: 0.8724 (p) cc_final: 0.8352 (t) REVERT: 0 36 LYS cc_start: 0.7608 (mmmm) cc_final: 0.7398 (mttm) REVERT: Z 26 LEU cc_start: 0.7147 (mm) cc_final: 0.6932 (mm) outliers start: 0 outliers final: 0 residues processed: 491 average time/residue: 0.7558 time to fit residues: 605.8028 Evaluate side-chains 370 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 213 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 271 optimal weight: 0.8980 overall best weight: 5.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: