Starting phenix.real_space_refine on Thu Dec 7 23:09:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/12_2023/6gc7_4382.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/12_2023/6gc7_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_4382/12_2023/6gc7_4382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/12_2023/6gc7_4382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/12_2023/6gc7_4382.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/12_2023/6gc7_4382.pdb" } 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 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-1.21rc1-5172/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: 21.25, per 1000 atoms: 0.39 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: 22.26 Conformation dependent library (CDL) restraints added in 2.1 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: 18.76 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: 50.85 Time building geometry restraints manager: 24.07 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 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: 32538 35.16 - 70.32: 3557 70.32 - 105.48: 497 105.48 - 140.64: 2 140.64 - 175.80: 7 Dihedral angle restraints: 36601 sinusoidal: 31663 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 36598 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 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: 0.740 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: 0.030 Extract box with map and model: 6.240 Check model and map are aligned: 0.620 Set scattering table: 0.390 Process input model: 153.060 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.740 ------------------------------------------------------------------------------- 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 : 21.690 175.805 33409 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 fitting. rotamer outliers: 4 poor density : 788 time to evaluate : 2.141 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: 787.2708 Evaluate side-chains 442 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 441 time to evaluate : 2.118 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3882 time to fit residues: 2.8460 ------------------------------------------------------------------------------- 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: 0.0870 overall best weight: 4.6176 ------------------------------------------------------------------------------- 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 115 GLN ** 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 76 HIS Q 43 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 86 GLN S 7 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** 0 3 GLN 0 41 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 59473 Z= 0.251 Angle : 0.594 10.734 89742 Z= 0.307 Chirality : 0.032 0.272 11603 Planarity : 0.005 0.112 4258 Dihedral : 22.601 178.441 30006 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.40 % Favored : 93.48 % Rotamer: Outliers : 0.14 % Allowed : 4.09 % Favored : 95.77 % 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: -1.86 (0.20), residues: 471 sheet: -1.15 (0.28), residues: 301 loop : -2.06 (0.17), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP Q 60 HIS 0.011 0.001 HIS P 55 PHE 0.014 0.002 PHE J 4 TYR 0.017 0.002 TYR Q 75 ARG 0.061 0.001 ARG K 18 *********************** 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 579 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 577 time to evaluate : 2.130 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 578 average time/residue: 0.5789 time to fit residues: 539.2786 Evaluate side-chains 419 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 2.110 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1205 ------------------------------------------------------------------------------- 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: 9.9990 chunk 221 optimal weight: 7.9990 chunk 89 optimal weight: 30.0000 chunk 325 optimal weight: 2.9990 chunk 351 optimal weight: 8.9990 chunk 290 optimal weight: 2.9990 chunk 322 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN T 15 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** Y 25 GLN ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 59473 Z= 0.313 Angle : 0.693 10.972 89742 Z= 0.360 Chirality : 0.037 0.259 11603 Planarity : 0.006 0.123 4258 Dihedral : 23.101 175.910 30006 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 27.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.29 % Favored : 92.60 % Rotamer: Outliers : 0.21 % Allowed : 5.43 % Favored : 94.36 % 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: -1.13 (0.22), residues: 468 sheet: -1.04 (0.27), residues: 333 loop : -1.86 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP Q 60 HIS 0.009 0.002 HIS P 55 PHE 0.027 0.003 PHE D 15 TYR 0.025 0.003 TYR Q 75 ARG 0.013 0.001 ARG 2 41 *********************** 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 537 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 534 time to evaluate : 2.181 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 outliers start: 3 outliers final: 1 residues processed: 537 average time/residue: 0.5808 time to fit residues: 508.2420 Evaluate side-chains 402 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 401 time to evaluate : 2.134 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4674 time to fit residues: 2.9661 ------------------------------------------------------------------------------- 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: 9.9990 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: 4.9990 chunk 326 optimal weight: 6.9990 chunk 346 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 309 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 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 185 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS 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 55 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN ** T 72 GLN ** 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 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 59473 Z= 0.332 Angle : 0.687 9.700 89742 Z= 0.356 Chirality : 0.038 0.236 11603 Planarity : 0.006 0.066 4258 Dihedral : 23.176 175.300 30006 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 28.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.99 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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: -2.24 (0.19), residues: 1702 helix: -1.14 (0.22), residues: 471 sheet: -0.92 (0.27), residues: 330 loop : -1.91 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP P 30 HIS 0.009 0.002 HIS 0 18 PHE 0.030 0.003 PHE K 79 TYR 0.023 0.002 TYR Q 44 ARG 0.011 0.001 ARG R 80 *********************** 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 495 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 2.161 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: 495 average time/residue: 0.5838 time to fit residues: 469.3997 Evaluate side-chains 392 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1047 ------------------------------------------------------------------------------- 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: 0.0970 chunk 196 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 295 optimal weight: 0.9990 chunk 239 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 310 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN K 13 ASN N 3 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 82 HIS S 60 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** 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: 0.6679 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 59473 Z= 0.161 Angle : 0.539 10.911 89742 Z= 0.279 Chirality : 0.031 0.271 11603 Planarity : 0.004 0.051 4258 Dihedral : 22.951 177.307 30006 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.70 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: -1.83 (0.19), residues: 1702 helix: -0.73 (0.23), residues: 486 sheet: -0.66 (0.28), residues: 312 loop : -1.69 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 30 HIS 0.011 0.001 HIS J 80 PHE 0.026 0.002 PHE K 79 TYR 0.013 0.001 TYR J 74 ARG 0.008 0.001 ARG K 64 *********************** 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 506 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 2.195 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 outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 0.5764 time to fit residues: 477.8380 Evaluate side-chains 391 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 2.167 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1359 ------------------------------------------------------------------------------- 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: 3.9990 chunk 68 optimal weight: 20.0000 chunk 203 optimal weight: 0.1980 chunk 85 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 287 optimal weight: 9.9990 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: 6.8392 ------------------------------------------------------------------------------- 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 9 ASN K 13 ASN L 35 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 82 HIS S 60 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.7392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 59473 Z= 0.323 Angle : 0.678 10.640 89742 Z= 0.350 Chirality : 0.038 0.291 11603 Planarity : 0.005 0.053 4258 Dihedral : 23.263 172.569 30006 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 29.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.34 % Favored : 90.54 % Rotamer: Outliers : 0.14 % Allowed : 2.75 % Favored : 97.11 % 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: -2.11 (0.19), residues: 1702 helix: -0.69 (0.24), residues: 464 sheet: -1.10 (0.27), residues: 323 loop : -1.90 (0.18), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP T 80 HIS 0.012 0.002 HIS J 80 PHE 0.047 0.003 PHE K 79 TYR 0.018 0.002 TYR S 38 ARG 0.011 0.001 ARG N 71 *********************** 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 469 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 467 time to evaluate : 2.136 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: 2 outliers final: 2 residues processed: 468 average time/residue: 0.5587 time to fit residues: 430.3717 Evaluate side-chains 379 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 377 time to evaluate : 2.152 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4390 time to fit residues: 3.7272 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 40.0000 chunk 197 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 195 optimal weight: 0.9990 chunk 291 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 345 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 210 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 132 HIS K 13 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS S 60 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.7464 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= 0.223 Angle : 0.582 10.722 89742 Z= 0.301 Chirality : 0.033 0.251 11603 Planarity : 0.005 0.060 4258 Dihedral : 23.108 174.127 30006 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 23.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.11 % Favored : 91.77 % Rotamer: Outliers : 0.07 % Allowed : 2.19 % Favored : 97.74 % 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: -2.05 (0.19), residues: 1702 helix: -0.66 (0.23), residues: 483 sheet: -1.13 (0.27), residues: 326 loop : -1.84 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 30 HIS 0.011 0.001 HIS J 80 PHE 0.024 0.002 PHE E 85 TYR 0.016 0.002 TYR S 38 ARG 0.007 0.001 ARG R 90 *********************** 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 475 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 474 time to evaluate : 2.214 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: 1 outliers final: 1 residues processed: 474 average time/residue: 0.5563 time to fit residues: 437.9825 Evaluate side-chains 374 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 373 time to evaluate : 2.145 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4573 time to fit residues: 2.9637 ------------------------------------------------------------------------------- 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: 20.0000 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: 7.9990 chunk 235 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 271 optimal weight: 0.0060 overall best weight: 7.6008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 76 HIS ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS ** K 5 GLN ** 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** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** 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 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 13 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.8173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 59473 Z= 0.359 Angle : 0.729 10.150 89742 Z= 0.375 Chirality : 0.040 0.276 11603 Planarity : 0.006 0.053 4258 Dihedral : 23.436 172.769 30006 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 32.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.87 % Favored : 90.01 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.50 (0.18), residues: 1702 helix: -1.16 (0.22), residues: 478 sheet: -1.40 (0.27), residues: 327 loop : -2.03 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP T 80 HIS 0.013 0.002 HIS J 80 PHE 0.040 0.004 PHE Q 56 TYR 0.025 0.003 TYR 0 47 ARG 0.011 0.001 ARG P 92 *********************** 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 464 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 464 time to evaluate : 2.162 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 outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.5411 time to fit residues: 422.1130 Evaluate side-chains 371 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 2.153 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1432 ------------------------------------------------------------------------------- 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: 0.6980 chunk 330 optimal weight: 5.9990 chunk 301 optimal weight: 5.9990 chunk 321 optimal weight: 20.0000 chunk 193 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 290 optimal weight: 0.7980 chunk 304 optimal weight: 10.0000 chunk 320 optimal weight: 4.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS J 132 HIS K 3 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** 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 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS ** S 57 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.8036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 59473 Z= 0.191 Angle : 0.575 12.509 89742 Z= 0.297 Chirality : 0.033 0.255 11603 Planarity : 0.005 0.051 4258 Dihedral : 23.178 173.165 30006 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.17 % Favored : 91.72 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.14 (0.19), residues: 1702 helix: -0.86 (0.23), residues: 479 sheet: -1.15 (0.29), residues: 297 loop : -1.82 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 30 HIS 0.008 0.002 HIS 0 41 PHE 0.042 0.002 PHE K 79 TYR 0.021 0.002 TYR S 38 ARG 0.010 0.001 ARG U 6 *********************** 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 482 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 482 time to evaluate : 2.189 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 outliers start: 0 outliers final: 0 residues processed: 482 average time/residue: 0.5612 time to fit residues: 449.8484 Evaluate side-chains 391 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 2.153 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1303 ------------------------------------------------------------------------------- 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: 5.9990 chunk 340 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 161 optimal weight: 20.0000 chunk 236 optimal weight: 0.9980 chunk 356 optimal weight: 10.0000 chunk 328 optimal weight: 10.0000 chunk 284 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 219 optimal weight: 0.9990 chunk 174 optimal weight: 50.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS K 5 GLN K 13 ASN L 35 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** 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 ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS S 57 ASN S 60 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.8002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 59473 Z= 0.163 Angle : 0.545 13.473 89742 Z= 0.280 Chirality : 0.031 0.233 11603 Planarity : 0.004 0.051 4258 Dihedral : 23.051 174.914 30006 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.46 % Favored : 91.48 % Rotamer: Outliers : 0.14 % Allowed : 0.49 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.91 (0.19), residues: 1702 helix: -0.68 (0.23), residues: 480 sheet: -0.89 (0.30), residues: 279 loop : -1.72 (0.18), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 30 HIS 0.012 0.001 HIS 0 41 PHE 0.033 0.002 PHE Q 78 TYR 0.017 0.002 TYR S 38 ARG 0.010 0.001 ARG K 64 ********************** 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 466 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 464 time to evaluate : 2.140 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 outliers start: 2 outliers final: 1 residues processed: 465 average time/residue: 0.5380 time to fit residues: 419.9517 Evaluate side-chains 386 residues out of total 1418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 385 time to evaluate : 2.172 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4318 time to fit residues: 2.9000 ------------------------------------------------------------------------------- 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: 9.9990 chunk 302 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 261 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 78 optimal weight: 40.0000 chunk 284 optimal weight: 5.9990 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: 8.5992 ------------------------------------------------------------------------------- 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 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** ** Q 80 ASN ** 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 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 13 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.062641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.042267 restraints weight = 324088.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.043837 restraints weight = 122847.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.044730 restraints weight = 74161.873| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.8788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 59473 Z= 0.392 Angle : 0.775 12.388 89742 Z= 0.397 Chirality : 0.042 0.241 11603 Planarity : 0.006 0.063 4258 Dihedral : 23.543 172.768 30006 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 37.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.63 % Favored : 89.25 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.65 (0.18), residues: 1702 helix: -1.39 (0.21), residues: 485 sheet: -1.30 (0.27), residues: 304 loop : -2.15 (0.18), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP T 80 HIS 0.013 0.003 HIS 0 41 PHE 0.045 0.003 PHE Q 56 TYR 0.022 0.003 TYR S 38 ARG 0.011 0.001 ARG Y 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8624.56 seconds wall clock time: 155 minutes 33.13 seconds (9333.13 seconds total)