Starting phenix.real_space_refine (version: dev) on Thu May 12 17:14:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/05_2022/6gc7_4382.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/05_2022/6gc7_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_4382/05_2022/6gc7_4382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/05_2022/6gc7_4382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/05_2022/6gc7_4382.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/05_2022/6gc7_4382.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 116": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 10": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 69": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 28": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 37": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'rna3p_pyr': 684, 'rna2p_pur': 182, 'rna3p_pur': 933, 'rna2p_pyr': 102} Link IDs: {'rna3p': 1616, 'rna2p': 284} 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: 22.76, per 1000 atoms: 0.42 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 - 3.50 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: 19.02 Conformation dependent library (CDL) restraints added in 2.2 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: 16.30 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: 49.27 Time building geometry restraints manager: 20.95 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: 99.78 - 106.62: 11512 106.62 - 113.47: 35418 113.47 - 120.31: 21850 120.31 - 127.15: 16302 127.15 - 134.00: 4660 Bond angle restraints: 89742 Sorted by residual: 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 angle pdb=" N VAL D 98 " pdb=" CA VAL D 98 " pdb=" C VAL D 98 " ideal model delta sigma weight residual 112.83 107.90 4.93 9.90e-01 1.02e+00 2.48e+01 ... (remaining 89737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 30307 35.16 - 70.32: 916 70.32 - 105.48: 73 105.48 - 140.64: 2 140.64 - 175.80: 7 Dihedral angle restraints: 31305 sinusoidal: 26367 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 31302 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 2.440 nonbonded pdb=" O2' U A 571 " pdb=" OP2 U A 573 " model vdw 2.268 2.440 nonbonded pdb=" O ILE S 35 " pdb=" OG1 THR S 39 " model vdw 2.281 2.440 nonbonded pdb=" O2' C A 239 " pdb=" O2' G A 622 " model vdw 2.284 2.440 ... (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 ========== 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 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. 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: 0.620 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: 7.880 Check model and map are aligned: 0.600 Convert atoms to be neutral: 0.350 Process input model: 145.190 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 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= 0.345 Chirality : 0.031 0.352 11603 Planarity : 0.004 0.063 4258 Dihedral : 13.130 175.805 28113 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.95 % Rotamer Outliers : 0.28 % 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 788 time to evaluate : 2.152 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 outliers start: 4 outliers final: 1 residues processed: 789 average time/residue: 0.6409 time to fit residues: 798.0504 Evaluate side-chains 441 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 440 time to evaluate : 2.127 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3778 time to fit residues: 2.8593 ------------------------------------------------------------------------------- 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: 6.9990 chunk 271 optimal weight: 8.9990 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: 6.9990 chunk 108 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 208 optimal weight: 0.0040 chunk 325 optimal weight: 8.9990 overall best weight: 6.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS J 132 HIS K 9 ASN ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 13 HIS Q 43 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 86 GLN S 7 HIS T 15 HIS U 44 HIS Y 15 ASN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.097 59473 Z= 0.341 Angle : 0.725 13.050 89742 Z= 0.373 Chirality : 0.038 0.460 11603 Planarity : 0.007 0.192 4258 Dihedral : 14.494 179.354 24710 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 27.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.17 % Favored : 92.66 % Rotamer Outliers : 0.28 % 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: -2.76 (0.18), residues: 1702 helix: -1.76 (0.20), residues: 485 sheet: -1.22 (0.29), residues: 301 loop : -2.10 (0.17), residues: 916 *********************** 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 546 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 542 time to evaluate : 2.149 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: symmetry clash outliers start: 4 outliers final: 1 residues processed: 544 average time/residue: 0.5541 time to fit residues: 486.7452 Evaluate side-chains 418 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 417 time to evaluate : 2.142 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3591 time to fit residues: 2.8514 ------------------------------------------------------------------------------- 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: 10.0000 chunk 221 optimal weight: 2.9990 chunk 89 optimal weight: 30.0000 chunk 325 optimal weight: 3.9990 chunk 351 optimal weight: 7.9990 chunk 290 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 HIS D 167 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN ** Z 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 59473 Z= 0.230 Angle : 0.568 11.957 89742 Z= 0.296 Chirality : 0.032 0.257 11603 Planarity : 0.005 0.070 4258 Dihedral : 14.358 179.424 24710 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.29 % Favored : 93.60 % Rotamer Outliers : 0.00 % 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: -2.15 (0.19), residues: 1702 helix: -1.04 (0.22), residues: 489 sheet: -0.89 (0.28), residues: 329 loop : -1.85 (0.19), residues: 884 *********************** 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 520 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 520 time to evaluate : 2.138 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.5671 time to fit residues: 476.3362 Evaluate side-chains 409 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 2.148 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1640 ------------------------------------------------------------------------------- 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: 2.9990 chunk 244 optimal weight: 20.0000 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: 8.9990 chunk 346 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 chunk 309 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 HIS ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN Y 15 ASN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 13 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 59473 Z= 0.247 Angle : 0.591 12.569 89742 Z= 0.307 Chirality : 0.033 0.240 11603 Planarity : 0.005 0.066 4258 Dihedral : 14.566 176.110 24710 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.34 % Favored : 92.54 % Rotamer Outliers : 0.00 % 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: -0.57 (0.23), residues: 472 sheet: -0.68 (0.29), residues: 308 loop : -1.75 (0.19), residues: 922 *********************** 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 493 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 493 time to evaluate : 2.789 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 outliers start: 0 outliers final: 0 residues processed: 493 average time/residue: 0.5472 time to fit residues: 442.7580 Evaluate side-chains 392 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 2.154 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1130 ------------------------------------------------------------------------------- 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: 9.9990 chunk 196 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 295 optimal weight: 10.0000 chunk 239 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 310 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN N 3 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.7013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 59473 Z= 0.331 Angle : 0.690 12.433 89742 Z= 0.357 Chirality : 0.038 0.236 11603 Planarity : 0.006 0.085 4258 Dihedral : 15.269 172.904 24710 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 29.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.75 % Favored : 91.13 % Rotamer Outliers : 0.00 % 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: -2.21 (0.19), residues: 1702 helix: -1.07 (0.22), residues: 477 sheet: -0.79 (0.27), residues: 319 loop : -1.96 (0.19), residues: 906 *********************** 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 482 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 482 time to evaluate : 2.599 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 outliers start: 0 outliers final: 0 residues processed: 482 average time/residue: 0.5491 time to fit residues: 433.5594 Evaluate side-chains 376 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 2.161 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1388 ------------------------------------------------------------------------------- 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: 0.0070 chunk 68 optimal weight: 10.0000 chunk 203 optimal weight: 40.0000 chunk 85 optimal weight: 10.0000 chunk 346 optimal weight: 0.9990 chunk 287 optimal weight: 6.9990 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: 5.6010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN K 3 GLN K 13 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS U 44 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN Y 20 ASN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 59473 Z= 0.268 Angle : 0.621 12.474 89742 Z= 0.322 Chirality : 0.035 0.237 11603 Planarity : 0.005 0.111 4258 Dihedral : 15.095 172.984 24710 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 25.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.58 % Favored : 91.30 % Rotamer Outliers : 0.00 % 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: -2.19 (0.19), residues: 1702 helix: -1.00 (0.22), residues: 496 sheet: -0.98 (0.26), residues: 335 loop : -1.90 (0.19), residues: 871 *********************** 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 486 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 time to evaluate : 2.175 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 outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.5407 time to fit residues: 430.4921 Evaluate side-chains 385 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.183 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1296 ------------------------------------------------------------------------------- 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: 6.9990 chunk 39 optimal weight: 40.0000 chunk 197 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 345 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 210 optimal weight: 0.5980 chunk 159 optimal weight: 10.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.7458 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= 0.214 Angle : 0.583 13.180 89742 Z= 0.301 Chirality : 0.033 0.251 11603 Planarity : 0.005 0.055 4258 Dihedral : 14.979 172.885 24710 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.28 % Favored : 91.60 % Rotamer Outliers : 0.00 % 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: -2.01 (0.19), residues: 1702 helix: -0.72 (0.23), residues: 482 sheet: -0.87 (0.28), residues: 316 loop : -1.85 (0.19), residues: 904 *********************** 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 465 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 2.219 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 outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.5318 time to fit residues: 409.4391 Evaluate side-chains 378 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 2.151 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1401 ------------------------------------------------------------------------------- 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: 9.9990 chunk 137 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 219 optimal weight: 0.0270 chunk 235 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 271 optimal weight: 0.9990 overall best weight: 6.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN K 13 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN S 60 HIS U 44 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.7972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.099 59473 Z= 0.298 Angle : 0.659 12.162 89742 Z= 0.340 Chirality : 0.037 0.263 11603 Planarity : 0.006 0.118 4258 Dihedral : 15.357 173.153 24710 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 28.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.87 % Favored : 90.07 % Rotamer Outliers : 0.07 % 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 (0.19), residues: 1702 helix: -1.09 (0.22), residues: 489 sheet: -1.02 (0.27), residues: 316 loop : -1.93 (0.19), residues: 897 *********************** REFINEMENT MACRO_CYCLE 8 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 445 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 444 time to evaluate : 2.200 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 outliers start: 1 outliers final: 1 residues processed: 445 average time/residue: 0.5298 time to fit residues: 394.2286 Evaluate side-chains 369 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 368 time to evaluate : 2.877 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4465 time to fit residues: 3.4929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 313 optimal weight: 0.9990 chunk 330 optimal weight: 7.9990 chunk 301 optimal weight: 3.9990 chunk 321 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 252 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 290 optimal weight: 2.9990 chunk 304 optimal weight: 7.9990 chunk 320 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS K 13 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN P 65 ASN ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN S 60 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN Y 20 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.7881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.181 59473 Z= 0.187 Angle : 0.570 13.424 89742 Z= 0.294 Chirality : 0.032 0.255 11603 Planarity : 0.005 0.099 4258 Dihedral : 14.960 173.288 24710 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.87 % Favored : 92.01 % Rotamer Outliers : 0.07 % 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: -1.99 (0.19), residues: 1702 helix: -0.70 (0.23), residues: 483 sheet: -1.04 (0.27), residues: 323 loop : -1.77 (0.19), residues: 896 *********************** REFINEMENT MACRO_CYCLE 9 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 458 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 457 time to evaluate : 2.154 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 outliers start: 1 outliers final: 0 residues processed: 457 average time/residue: 0.5250 time to fit residues: 400.6940 Evaluate side-chains 373 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 2.202 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 211 optimal weight: 1.9990 chunk 340 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 236 optimal weight: 8.9990 chunk 356 optimal weight: 20.0000 chunk 328 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 219 optimal weight: 7.9990 chunk 174 optimal weight: 50.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 80 HIS K 13 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.7960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.421 59473 Z= 0.223 Angle : 0.586 24.319 89742 Z= 0.305 Chirality : 0.033 0.266 11603 Planarity : 0.005 0.136 4258 Dihedral : 14.967 173.605 24710 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.99 % Favored : 90.89 % Rotamer Outliers : 0.00 % 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: -1.95 (0.19), residues: 1702 helix: -0.69 (0.23), residues: 481 sheet: -0.97 (0.27), residues: 323 loop : -1.76 (0.19), residues: 898 ********************** REFINEMENT MACRO_CYCLE 10 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 441 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 2.244 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 outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.5204 time to fit residues: 384.8241 Evaluate side-chains 369 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 2.192 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 225 optimal weight: 0.3980 chunk 302 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 41 optimal weight: 30.0000 chunk 78 optimal weight: 40.0000 chunk 284 optimal weight: 0.7980 chunk 119 optimal weight: 30.0000 chunk 292 optimal weight: 9.9990 chunk 36 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 overall best weight: 3.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS K 13 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN S 60 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN Y 20 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.066812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.046155 restraints weight = 308497.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.047872 restraints weight = 115073.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.048866 restraints weight = 67984.567| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.8070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 59473 Z= 0.196 Angle : 0.568 12.202 89742 Z= 0.292 Chirality : 0.032 0.264 11603 Planarity : 0.005 0.072 4258 Dihedral : 14.928 173.730 24710 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.81 % Favored : 91.07 % Rotamer Outliers : 0.07 % 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: -1.90 (0.19), residues: 1702 helix: -0.65 (0.24), residues: 481 sheet: -0.89 (0.27), residues: 311 loop : -1.74 (0.19), residues: 910 =============================================================================== Job complete usr+sys time: 7899.51 seconds wall clock time: 142 minutes 42.37 seconds (8562.37 seconds total)