Starting phenix.real_space_refine on Mon Sep 30 01:57:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc4_4380/09_2024/6gc4_4380.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc4_4380/09_2024/6gc4_4380.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/6gc4_4380/09_2024/6gc4_4380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc4_4380/09_2024/6gc4_4380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc4_4380/09_2024/6gc4_4380.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc4_4380/09_2024/6gc4_4380.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.164 sd= 1.303 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 2705 5.49 5 S 62 5.16 5 C 39724 2.51 5 N 14967 2.21 5 O 22707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 80165 Number of models: 1 Model: "" Number of chains: 26 Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "A" Number of atoms: 55544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2586, 55544 Classifications: {'RNA': 2586} Modifications used: {'rna2p_pur': 251, 'rna2p_pyr': 131, 'rna3p_pur': 1252, 'rna3p_pyr': 952} Link IDs: {'rna2p': 382, 'rna3p': 2203} Chain breaks: 6 Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} 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: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} 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: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} 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: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} 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: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "F" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} 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} Chain: "H" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 384 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 32.80, per 1000 atoms: 0.41 Number of scatterers: 80165 At special positions: 0 Unit cell: (220.72, 207.08, 219.48, 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 62 16.00 P 2705 15.00 O 22707 8.00 N 14967 7.00 C 39724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.73 Conformation dependent library (CDL) restraints added in 3.3 seconds 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5164 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 40 sheets defined 27.5% alpha, 18.7% beta 816 base pairs and 1437 stacking pairs defined. Time for finding SS restraints: 30.40 Creating SS restraints... Processing helix chain 'V' and resid 13 through 22 removed outlier: 3.829A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 51 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 196 through 202 removed outlier: 4.348A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.935A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.837A pdb=" N LYS D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY D 72 " --> pdb=" O PHE D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.500A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 36 removed outlier: 3.590A pdb=" N ALA E 36 " --> pdb=" O VAL E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 40 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.556A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 removed outlier: 3.622A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.586A pdb=" N LEU E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 201 Processing helix chain 'G' and resid 60 through 78 removed outlier: 3.789A pdb=" N ALA G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY G 65 " --> pdb=" O TRP G 61 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G 78 " --> pdb=" O MET G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.203A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.549A pdb=" N LYS J 61 " --> pdb=" O ASN J 58 " (cutoff:3.500A) removed outlier: 3.642A 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 89 through 96 removed outlier: 3.832A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 107 removed outlier: 4.352A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 120 Processing helix chain 'K' and resid 113 through 118 Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.802A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 137 removed outlier: 4.390A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.772A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET N 20 " --> pdb=" O HIS N 16 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER N 27 " --> pdb=" O ASN N 23 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS N 31 " --> pdb=" O SER N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 55 removed outlier: 3.977A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 removed outlier: 3.605A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 79 removed outlier: 3.892A pdb=" N LYS N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 removed outlier: 3.626A pdb=" N ARG N 86 " --> pdb=" O GLU N 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 10 removed outlier: 3.973A pdb=" N GLN P 6 " --> pdb=" O ASN P 2 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 3.754A 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 100 removed outlier: 3.731A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 107 Processing helix chain 'Q' and resid 5 through 18 removed outlier: 3.519A pdb=" N ARG Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS Q 14 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 28 removed outlier: 4.084A pdb=" N ARG Q 27 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.295A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN Q 58 " --> pdb=" O ARG Q 54 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 84 removed outlier: 3.615A pdb=" N ASN Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.670A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 117 Processing helix chain 'S' and resid 14 through 22 removed outlier: 3.868A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP S 22 " --> pdb=" O ARG S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 25 No H-bonds generated for 'chain 'S' and resid 23 through 25' Processing helix chain 'S' and resid 28 through 38 removed outlier: 4.064A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 60 removed outlier: 4.093A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS S 49 " --> pdb=" O VAL S 45 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 removed outlier: 3.762A pdb=" N ASP S 68 " --> pdb=" O ASP S 65 " (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 8 Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.837A 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 'X' and resid 52 through 61 Processing helix chain 'X' and resid 62 through 71 removed outlier: 3.666A pdb=" N VAL X 66 " --> pdb=" O GLY X 62 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU X 69 " --> pdb=" O THR X 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 34 removed outlier: 4.558A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET Y 30 " --> pdb=" O PHE Y 26 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA Y 32 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 45 removed outlier: 4.121A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN Y 45 " --> pdb=" O HIS Y 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 40 through 45' Processing helix chain 'Y' and resid 46 through 56 removed outlier: 3.655A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 16 Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 23 removed outlier: 3.509A pdb=" N ARG 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 Processing helix chain 'O' and resid 3 through 18 removed outlier: 4.854A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 62 removed outlier: 3.819A pdb=" N GLN O 61 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU O 62 " --> pdb=" O ALA O 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 58 through 62' Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 113 removed outlier: 3.695A pdb=" N ALA O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 11 through 19 removed outlier: 4.105A pdb=" N LEU F 15 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 removed outlier: 3.847A pdb=" N VAL F 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 60 removed outlier: 4.073A pdb=" N LEU F 49 " --> pdb=" O ASP F 45 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 removed outlier: 4.317A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE F 98 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 137 removed outlier: 3.831A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE F 137 " --> pdb=" O GLN F 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 133 through 137' Processing helix chain 'F' and resid 141 through 145 removed outlier: 3.839A pdb=" N VAL F 145 " --> pdb=" O TYR F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 172 removed outlier: 4.014A pdb=" N GLY F 165 " --> pdb=" O SER F 161 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.567A pdb=" N ALA Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 30 removed outlier: 3.639A pdb=" N ALA H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 50 Processing sheet with id=AA1, first strand: chain 'V' and resid 2 through 5 removed outlier: 5.576A pdb=" N PHE V 2 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL V 64 " --> pdb=" O PHE V 2 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ALA V 74 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL V 92 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 7 through 8 removed outlier: 3.603A pdb=" N PHE V 26 " --> pdb=" O LEU V 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.602A pdb=" N GLU C 34 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR C 61 " --> pdb=" O GLU C 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 104 removed outlier: 3.782A pdb=" N ARG C 101 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 128 through 130 removed outlier: 7.223A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET C 180 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AA8, first strand: chain 'D' and resid 169 through 175 removed outlier: 5.920A pdb=" N VAL D 107 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR D 25 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.253A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE D 82 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG D 33 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 32 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 3 Processing sheet with id=AB2, first strand: chain 'E' and resid 118 through 121 removed outlier: 5.977A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU E 147 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N THR E 189 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ILE E 149 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 8 through 9 removed outlier: 4.213A pdb=" N VAL G 8 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR G 50 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS G 43 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY G 52 " --> pdb=" O GLU G 41 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU G 41 " --> pdb=" O GLY G 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 17 through 18 removed outlier: 3.853A pdb=" N ILE G 23 " --> pdb=" O ARG G 34 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG G 34 " --> pdb=" O ILE G 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 121 through 123 removed outlier: 3.867A pdb=" N THR G 121 " --> pdb=" O LYS G 133 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS G 133 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU G 123 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL G 131 " --> pdb=" O GLU G 123 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY G 134 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN G 87 " --> pdb=" O ARG G 162 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG G 162 " --> pdb=" O GLN G 87 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL G 89 " --> pdb=" O GLY G 160 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY G 160 " --> pdb=" O VAL G 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 94 through 96 removed outlier: 3.565A pdb=" N ARG G 94 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA G 96 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE G 102 " --> pdb=" O HIS G 114 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS G 114 " --> pdb=" O ILE G 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.750A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 73 through 76 removed outlier: 3.586A pdb=" N ALA J 87 " --> pdb=" O TYR J 74 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS J 76 " --> pdb=" O LYS J 85 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS J 85 " --> pdb=" O HIS J 76 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 6 through 10 removed outlier: 3.950A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU K 58 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL K 63 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 69 through 70 removed outlier: 4.169A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE P 58 " --> pdb=" O PHE P 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS P 36 " --> pdb=" O GLU P 33 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 121 through 123 Processing sheet with id=AC3, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.872A pdb=" N ILE N 34 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE N 113 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR N 36 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.915A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N TYR R 2 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE R 41 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 19 through 22 removed outlier: 3.632A pdb=" N VAL R 20 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL R 96 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE R 101 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL R 58 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 72 through 78 removed outlier: 3.521A pdb=" N VAL R 72 " --> pdb=" O HIS R 89 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS R 89 " --> pdb=" O VAL R 72 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'S' and resid 3 through 7 removed outlier: 6.677A pdb=" N ASP S 94 " --> pdb=" O ILE S 85 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE S 85 " --> pdb=" O ASP S 94 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE S 96 " --> pdb=" O LYS S 83 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS S 83 " --> pdb=" O ILE S 96 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LYS S 98 " --> pdb=" O SER S 81 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER S 81 " --> pdb=" O LYS S 98 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR S 104 " --> pdb=" O PHE S 75 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE S 75 " --> pdb=" O THR S 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 11 through 14 removed outlier: 3.854A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP T 80 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.761A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY U 22 " --> pdb=" O VAL U 10 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'U' and resid 40 through 45 removed outlier: 3.888A pdb=" N VAL U 41 " --> pdb=" O LYS U 60 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS U 43 " --> pdb=" O VAL U 58 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL U 58 " --> pdb=" O LYS U 43 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN U 45 " --> pdb=" O GLY U 56 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY U 56 " --> pdb=" O GLN U 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'U' and resid 82 through 85 removed outlier: 3.895A pdb=" N ARG U 85 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 12 through 15 removed outlier: 3.982A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.740A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AD6, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AD7, first strand: chain 'O' and resid 47 through 50 removed outlier: 7.223A pdb=" N VAL O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA O 50 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA O 37 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 65 through 66 removed outlier: 4.173A pdb=" N CYS F 86 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 90 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE F 33 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR F 156 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE F 33 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR F 154 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU F 35 " --> pdb=" O ASP F 152 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP F 152 " --> pdb=" O LEU F 35 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR F 127 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.706A pdb=" N ARG Z 37 " --> pdb=" O ILE Z 4 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.974A pdb=" N ILE H 4 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL H 37 " --> pdb=" O ILE H 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'W' and resid 18 through 19 removed outlier: 4.013A pdb=" N GLY W 18 " --> pdb=" O ARG W 35 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 42 through 43 removed outlier: 6.511A pdb=" N HIS W 42 " --> pdb=" O ILE W 76 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ILE W 78 " --> pdb=" O HIS W 42 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 47 through 49 removed outlier: 3.857A pdb=" N GLY W 48 " --> pdb=" O PHE W 56 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 620 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2073 hydrogen bonds 3286 hydrogen bond angles 0 basepair planarities 816 basepair parallelities 1437 stacking parallelities Total time for adding SS restraints: 130.73 Time building geometry restraints manager: 17.20 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: 12151 1.33 - 1.45: 37454 1.45 - 1.57: 32306 1.57 - 1.69: 5403 1.69 - 1.82: 115 Bond restraints: 87429 Sorted by residual: bond pdb=" C LEU N 38 " pdb=" N PRO N 39 " ideal model delta sigma weight residual 1.336 1.385 -0.050 1.23e-02 6.61e+03 1.63e+01 bond pdb=" CA GLN Y 39 " pdb=" CB GLN Y 39 " ideal model delta sigma weight residual 1.527 1.580 -0.052 1.30e-02 5.92e+03 1.62e+01 bond pdb=" C GLU N 49 " pdb=" N PRO N 50 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.19e-02 7.06e+03 1.27e+01 bond pdb=" C LYS C 124 " pdb=" N PRO C 125 " ideal model delta sigma weight residual 1.333 1.359 -0.025 1.01e-02 9.80e+03 6.34e+00 bond pdb=" C ARG K 71 " pdb=" N PRO K 72 " ideal model delta sigma weight residual 1.337 1.361 -0.024 9.80e-03 1.04e+04 6.16e+00 ... (remaining 87424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.10: 131456 8.10 - 16.19: 20 16.19 - 24.29: 2 24.29 - 32.38: 2 32.38 - 40.48: 2 Bond angle restraints: 131482 Sorted by residual: angle pdb=" OP1 A A2439 " pdb=" P A A2439 " pdb=" OP2 A A2439 " ideal model delta sigma weight residual 119.60 79.12 40.48 3.00e+00 1.11e-01 1.82e+02 angle pdb=" O3' U A2438 " pdb=" P A A2439 " pdb=" OP2 A A2439 " ideal model delta sigma weight residual 108.00 71.38 36.62 3.00e+00 1.11e-01 1.49e+02 angle pdb=" OP1 A A2439 " pdb=" P A A2439 " pdb=" O5' A A2439 " ideal model delta sigma weight residual 108.00 78.20 29.80 3.00e+00 1.11e-01 9.87e+01 angle pdb=" C ARG H 27 " pdb=" N ASN H 28 " pdb=" CA ASN H 28 " ideal model delta sigma weight residual 121.54 139.35 -17.81 1.91e+00 2.74e-01 8.69e+01 angle pdb=" O3' U A2438 " pdb=" P A A2439 " pdb=" OP1 A A2439 " ideal model delta sigma weight residual 108.00 135.86 -27.86 3.00e+00 1.11e-01 8.62e+01 ... (remaining 131477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 49132 35.58 - 71.16: 6111 71.16 - 106.75: 709 106.75 - 142.33: 9 142.33 - 177.91: 8 Dihedral angle restraints: 55969 sinusoidal: 47941 harmonic: 8028 Sorted by residual: dihedral pdb=" CA VAL H 31 " pdb=" C VAL H 31 " pdb=" N PRO H 32 " pdb=" CA PRO H 32 " ideal model delta harmonic sigma weight residual -180.00 -113.04 -66.96 0 5.00e+00 4.00e-02 1.79e+02 dihedral pdb=" CA THR D 151 " pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta harmonic sigma weight residual -180.00 -121.58 -58.42 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA PHE F 174 " pdb=" C PHE F 174 " pdb=" N PRO F 175 " pdb=" CA PRO F 175 " ideal model delta harmonic sigma weight residual -180.00 -127.54 -52.46 0 5.00e+00 4.00e-02 1.10e+02 ... (remaining 55966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 16204 0.080 - 0.161: 635 0.161 - 0.241: 40 0.241 - 0.322: 6 0.322 - 0.402: 2 Chirality restraints: 16887 Sorted by residual: chirality pdb=" CB ILE J 84 " pdb=" CA ILE J 84 " pdb=" CG1 ILE J 84 " pdb=" CG2 ILE J 84 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" C3' U A2092 " pdb=" C4' U A2092 " pdb=" O3' U A2092 " pdb=" C2' U A2092 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C1' C A2196 " pdb=" O4' C A2196 " pdb=" C2' C A2196 " pdb=" N1 C A2196 " both_signs ideal model delta sigma weight residual False 2.47 2.15 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 16884 not shown) Planarity restraints: 6592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 151 " 0.063 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO D 152 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 152 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 152 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS Y 44 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C LYS Y 44 " -0.052 2.00e-02 2.50e+03 pdb=" O LYS Y 44 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN Y 45 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A2196 " -0.035 2.00e-02 2.50e+03 1.89e-02 8.04e+00 pdb=" N1 C A2196 " 0.043 2.00e-02 2.50e+03 pdb=" C2 C A2196 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C A2196 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C A2196 " 0.000 2.00e-02 2.50e+03 pdb=" C4 C A2196 " -0.006 2.00e-02 2.50e+03 pdb=" N4 C A2196 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C A2196 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C A2196 " 0.006 2.00e-02 2.50e+03 ... (remaining 6589 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 15711 2.78 - 3.31: 63623 3.31 - 3.84: 168464 3.84 - 4.37: 194003 4.37 - 4.90: 259856 Nonbonded interactions: 701657 Sorted by model distance: nonbonded pdb=" O6 G A1168 " pdb=" O2 U A1181 " model vdw 2.252 2.432 nonbonded pdb=" O2' G A 561 " pdb=" OH TYR Q 44 " model vdw 2.265 3.040 nonbonded pdb=" O2' A A1794 " pdb=" O2' A A1900 " model vdw 2.276 3.040 nonbonded pdb=" OP2 G A 411 " pdb=" O2' A A2406 " model vdw 2.278 3.040 nonbonded pdb=" O2 C A1999 " pdb=" O2' U A2687 " model vdw 2.283 3.040 ... (remaining 701652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.090 Extract box with map and model: 2.290 Check model and map are aligned: 0.460 Set scattering table: 0.580 Process input model: 248.000 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.270 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: 0.030 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 256.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 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 0.052 87429 Z= 0.180 Angle : 0.766 40.479 131482 Z= 0.402 Chirality : 0.034 0.402 16887 Planarity : 0.005 0.095 6592 Dihedral : 22.716 177.910 50805 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.89 % Favored : 92.90 % Rotamer: Outliers : 0.39 % Allowed : 5.58 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 4.65 % Twisted General : 0.26 % 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: -3.77 (0.13), residues: 2788 helix: -3.23 (0.13), residues: 695 sheet: -1.29 (0.22), residues: 491 loop : -2.63 (0.12), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP C 212 HIS 0.007 0.001 HIS N 16 PHE 0.022 0.002 PHE U 94 TYR 0.018 0.002 TYR F 21 ARG 0.011 0.001 ARG 0 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 985 time to evaluate : 3.264 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: V 50 MET cc_start: 0.2528 (mtp) cc_final: 0.1713 (tpt) REVERT: C 212 TRP cc_start: 0.6771 (p90) cc_final: 0.6224 (p90) REVERT: D 95 SER cc_start: 0.7860 (m) cc_final: 0.7641 (p) REVERT: D 125 TRP cc_start: 0.6689 (m100) cc_final: 0.6194 (m100) REVERT: E 105 LEU cc_start: 0.5666 (mt) cc_final: 0.5442 (mt) REVERT: J 121 LYS cc_start: 0.7136 (mtpm) cc_final: 0.6902 (mtpm) REVERT: K 9 ASN cc_start: 0.6135 (m-40) cc_final: 0.5870 (m-40) REVERT: K 86 LEU cc_start: 0.5744 (mt) cc_final: 0.5443 (mt) REVERT: N 52 ILE cc_start: 0.8953 (mt) cc_final: 0.8727 (mm) REVERT: P 99 LEU cc_start: 0.8507 (mt) cc_final: 0.8289 (tt) REVERT: R 10 LYS cc_start: 0.5171 (pmmt) cc_final: 0.3594 (pttm) REVERT: R 24 LYS cc_start: 0.7973 (tmmt) cc_final: 0.7531 (tptp) REVERT: R 90 ARG cc_start: 0.5749 (mtp-110) cc_final: 0.5458 (mmm-85) REVERT: R 92 TRP cc_start: 0.6388 (m100) cc_final: 0.5890 (m100) REVERT: S 30 SER cc_start: 0.8193 (p) cc_final: 0.7294 (p) REVERT: S 76 VAL cc_start: 0.5531 (t) cc_final: 0.5157 (t) REVERT: U 30 SER cc_start: 0.8343 (p) cc_final: 0.7935 (t) REVERT: 2 16 HIS cc_start: 0.7818 (m-70) cc_final: 0.7486 (m-70) REVERT: O 26 LEU cc_start: 0.5971 (tp) cc_final: 0.5419 (tp) REVERT: O 40 ILE cc_start: 0.7926 (mt) cc_final: 0.7721 (mp) outliers start: 9 outliers final: 1 residues processed: 992 average time/residue: 0.8936 time to fit residues: 1423.8537 Evaluate side-chains 532 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 531 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 458 optimal weight: 7.9990 chunk 411 optimal weight: 0.0030 chunk 228 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 277 optimal weight: 9.9990 chunk 219 optimal weight: 30.0000 chunk 425 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 316 optimal weight: 20.0000 chunk 493 optimal weight: 10.0000 overall best weight: 7.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 87 GLN ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN L 35 HIS L 54 GLN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN Q 71 ASN R 12 HIS R 43 ASN R 66 HIS R 89 HIS S 7 HIS ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN ** X 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN O 29 HIS O 100 HIS ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 42 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 87429 Z= 0.372 Angle : 0.852 41.789 131482 Z= 0.426 Chirality : 0.042 0.280 16887 Planarity : 0.007 0.102 6592 Dihedral : 23.770 178.163 45294 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.39 % Favored : 91.43 % Rotamer: Outliers : 0.44 % Allowed : 4.97 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.14), residues: 2788 helix: -1.87 (0.17), residues: 724 sheet: -1.22 (0.24), residues: 436 loop : -2.22 (0.13), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP C 212 HIS 0.016 0.002 HIS C 24 PHE 0.041 0.003 PHE Q 56 TYR 0.023 0.003 TYR K 32 ARG 0.025 0.001 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 674 time to evaluate : 3.255 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: V 50 MET cc_start: 0.3345 (mtp) cc_final: 0.2406 (tpt) REVERT: C 63 ILE cc_start: 0.8487 (mm) cc_final: 0.8284 (mt) REVERT: C 173 LEU cc_start: 0.8244 (pp) cc_final: 0.8031 (pp) REVERT: D 29 VAL cc_start: 0.7600 (p) cc_final: 0.7315 (p) REVERT: J 50 THR cc_start: 0.8938 (m) cc_final: 0.8724 (m) REVERT: J 101 ILE cc_start: 0.8788 (mp) cc_final: 0.8432 (mp) REVERT: J 108 MET cc_start: 0.7760 (mtm) cc_final: 0.7529 (mtp) REVERT: L 127 VAL cc_start: 0.7898 (t) cc_final: 0.7587 (m) REVERT: N 117 ASP cc_start: 0.6618 (p0) cc_final: 0.6232 (p0) REVERT: P 54 LEU cc_start: 0.6834 (tp) cc_final: 0.6567 (tp) REVERT: Q 82 LEU cc_start: 0.7703 (mt) cc_final: 0.7493 (mt) REVERT: R 39 LEU cc_start: 0.7714 (mm) cc_final: 0.7384 (tp) REVERT: S 30 SER cc_start: 0.8869 (p) cc_final: 0.7694 (t) REVERT: 0 14 MET cc_start: 0.7650 (mtt) cc_final: 0.7446 (mpp) REVERT: F 146 ASP cc_start: 0.5337 (t70) cc_final: 0.4491 (m-30) REVERT: W 79 GLU cc_start: 0.6179 (mt-10) cc_final: 0.5729 (mt-10) outliers start: 10 outliers final: 5 residues processed: 680 average time/residue: 0.8798 time to fit residues: 1006.9844 Evaluate side-chains 510 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 505 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 274 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 410 optimal weight: 5.9990 chunk 335 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 493 optimal weight: 9.9990 chunk 533 optimal weight: 4.9990 chunk 439 optimal weight: 0.5980 chunk 489 optimal weight: 30.0000 chunk 168 optimal weight: 10.0000 chunk 396 optimal weight: 2.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 GLN ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN U 39 ASN U 65 GLN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN W 8 ASN W 53 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 87429 Z= 0.207 Angle : 0.644 43.222 131482 Z= 0.323 Chirality : 0.035 0.403 16887 Planarity : 0.006 0.091 6592 Dihedral : 23.623 177.274 45294 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.50 % Favored : 92.36 % Rotamer: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.14), residues: 2788 helix: -1.11 (0.18), residues: 735 sheet: -1.08 (0.24), residues: 439 loop : -2.13 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 212 HIS 0.017 0.002 HIS J 80 PHE 0.022 0.002 PHE U 95 TYR 0.019 0.002 TYR E 101 ARG 0.009 0.001 ARG X 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 647 time to evaluate : 3.230 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: V 1 MET cc_start: 0.5377 (pmm) cc_final: 0.4458 (pmm) REVERT: V 50 MET cc_start: 0.2894 (mtp) cc_final: 0.2122 (tpt) REVERT: C 63 ILE cc_start: 0.8665 (mm) cc_final: 0.8359 (mt) REVERT: C 83 ASP cc_start: 0.7626 (t0) cc_final: 0.6756 (t0) REVERT: C 90 ILE cc_start: 0.7682 (pt) cc_final: 0.7167 (mt) REVERT: C 116 GLN cc_start: 0.7186 (pm20) cc_final: 0.6979 (pm20) REVERT: C 224 MET cc_start: 0.6022 (mtp) cc_final: 0.5499 (mtt) REVERT: D 156 PHE cc_start: 0.6120 (m-10) cc_final: 0.5841 (m-10) REVERT: E 55 SER cc_start: 0.8614 (p) cc_final: 0.8210 (p) REVERT: E 97 ASN cc_start: 0.7177 (m-40) cc_final: 0.5850 (m-40) REVERT: J 60 ASP cc_start: 0.8072 (p0) cc_final: 0.7453 (t0) REVERT: J 101 ILE cc_start: 0.8811 (mp) cc_final: 0.8363 (mt) REVERT: J 108 MET cc_start: 0.7971 (mtm) cc_final: 0.7683 (mtp) REVERT: K 8 LEU cc_start: 0.7973 (mp) cc_final: 0.6977 (mp) REVERT: L 127 VAL cc_start: 0.7998 (t) cc_final: 0.7775 (m) REVERT: Q 54 ARG cc_start: 0.9113 (mtt-85) cc_final: 0.8713 (ttm170) REVERT: R 32 THR cc_start: 0.7103 (m) cc_final: 0.5385 (m) REVERT: R 71 LYS cc_start: 0.7027 (ttmt) cc_final: 0.6742 (ttmt) REVERT: S 30 SER cc_start: 0.8663 (p) cc_final: 0.8103 (t) REVERT: S 84 ARG cc_start: 0.8422 (mmp80) cc_final: 0.8197 (mmp80) REVERT: 0 53 VAL cc_start: 0.8418 (m) cc_final: 0.8026 (t) REVERT: 2 15 SER cc_start: 0.7473 (p) cc_final: 0.6406 (p) REVERT: 2 16 HIS cc_start: 0.8063 (m-70) cc_final: 0.7145 (m-70) REVERT: O 26 LEU cc_start: 0.5286 (tp) cc_final: 0.5036 (tp) REVERT: O 89 ASP cc_start: 0.6580 (m-30) cc_final: 0.6290 (t0) REVERT: F 146 ASP cc_start: 0.4776 (t70) cc_final: 0.4467 (t0) outliers start: 1 outliers final: 0 residues processed: 647 average time/residue: 0.8117 time to fit residues: 879.3653 Evaluate side-chains 501 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 488 optimal weight: 9.9990 chunk 371 optimal weight: 7.9990 chunk 256 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 235 optimal weight: 30.0000 chunk 331 optimal weight: 0.4980 chunk 495 optimal weight: 0.3980 chunk 524 optimal weight: 20.0000 chunk 259 optimal weight: 10.0000 chunk 469 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 overall best weight: 5.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 ASN R 12 HIS R 86 GLN ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 HIS ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 87429 Z= 0.256 Angle : 0.668 12.642 131482 Z= 0.345 Chirality : 0.037 0.272 16887 Planarity : 0.006 0.112 6592 Dihedral : 23.657 178.240 45294 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.33 % Favored : 90.53 % Rotamer: Outliers : 0.04 % Allowed : 4.32 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % Twisted General : 0.11 % 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: -2.39 (0.15), residues: 2788 helix: -0.94 (0.19), residues: 713 sheet: -1.09 (0.24), residues: 462 loop : -2.10 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP C 212 HIS 0.020 0.002 HIS J 80 PHE 0.020 0.002 PHE W 22 TYR 0.022 0.002 TYR E 101 ARG 0.009 0.001 ARG X 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 624 time to evaluate : 3.213 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: V 1 MET cc_start: 0.5519 (pmm) cc_final: 0.4838 (pmm) REVERT: C 71 ASP cc_start: 0.8026 (m-30) cc_final: 0.7763 (m-30) REVERT: C 145 MET cc_start: 0.7421 (mmm) cc_final: 0.6920 (mmm) REVERT: C 212 TRP cc_start: 0.7642 (p90) cc_final: 0.7215 (p90) REVERT: C 224 MET cc_start: 0.6571 (mtp) cc_final: 0.6045 (mtp) REVERT: E 55 SER cc_start: 0.8697 (p) cc_final: 0.8321 (p) REVERT: E 97 ASN cc_start: 0.6980 (m-40) cc_final: 0.5749 (m-40) REVERT: J 60 ASP cc_start: 0.8222 (p0) cc_final: 0.7959 (t0) REVERT: J 131 ASN cc_start: 0.5749 (p0) cc_final: 0.5521 (p0) REVERT: L 127 VAL cc_start: 0.8125 (t) cc_final: 0.7842 (m) REVERT: N 20 MET cc_start: 0.7701 (tpp) cc_final: 0.7450 (tpt) REVERT: P 40 GLN cc_start: 0.4682 (mm-40) cc_final: 0.4398 (mm-40) REVERT: P 99 LEU cc_start: 0.8935 (mt) cc_final: 0.8721 (tt) REVERT: Q 54 ARG cc_start: 0.9029 (mtt-85) cc_final: 0.8725 (ttm170) REVERT: R 1 MET cc_start: 0.4553 (tpt) cc_final: 0.4147 (ptp) REVERT: R 39 LEU cc_start: 0.7380 (mp) cc_final: 0.7101 (mp) REVERT: R 91 GLN cc_start: 0.8649 (tp40) cc_final: 0.7845 (tp-100) REVERT: R 97 LYS cc_start: 0.5507 (ttpp) cc_final: 0.5258 (ttpp) REVERT: S 30 SER cc_start: 0.8693 (p) cc_final: 0.8093 (t) REVERT: T 5 GLU cc_start: 0.7469 (mp0) cc_final: 0.6406 (tm-30) REVERT: U 30 SER cc_start: 0.8649 (p) cc_final: 0.8428 (p) REVERT: 0 53 VAL cc_start: 0.8170 (m) cc_final: 0.7793 (t) REVERT: 2 3 ARG cc_start: 0.7620 (mmt180) cc_final: 0.7190 (mmt180) REVERT: 2 15 SER cc_start: 0.7415 (p) cc_final: 0.7057 (p) REVERT: 2 31 LEU cc_start: 0.8873 (mm) cc_final: 0.8665 (mm) REVERT: O 76 LYS cc_start: 0.7673 (mttt) cc_final: 0.7227 (mttp) REVERT: W 20 LYS cc_start: 0.8155 (ptpp) cc_final: 0.7740 (mttm) REVERT: W 64 LYS cc_start: 0.7680 (ttmt) cc_final: 0.7382 (ttmt) REVERT: W 79 GLU cc_start: 0.5781 (mt-10) cc_final: 0.5561 (mt-10) outliers start: 1 outliers final: 0 residues processed: 625 average time/residue: 0.8197 time to fit residues: 858.9217 Evaluate side-chains 493 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 493 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 437 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 390 optimal weight: 0.3980 chunk 216 optimal weight: 20.0000 chunk 447 optimal weight: 7.9990 chunk 362 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 268 optimal weight: 8.9990 chunk 471 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 88 HIS ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN D 150 GLN E 46 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN P 55 HIS ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN R 43 ASN ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN U 39 ASN 0 4 GLN ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN Z 48 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 87429 Z= 0.203 Angle : 0.601 12.679 131482 Z= 0.312 Chirality : 0.035 0.270 16887 Planarity : 0.005 0.086 6592 Dihedral : 23.604 178.384 45294 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.54 % Favored : 91.32 % Rotamer: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % Twisted General : 0.11 % 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: -2.12 (0.15), residues: 2788 helix: -0.64 (0.19), residues: 716 sheet: -0.83 (0.23), residues: 494 loop : -2.03 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 212 HIS 0.007 0.001 HIS J 132 PHE 0.038 0.002 PHE Q 56 TYR 0.018 0.002 TYR 0 47 ARG 0.009 0.001 ARG T 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 621 time to evaluate : 3.239 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: V 1 MET cc_start: 0.5485 (pmm) cc_final: 0.4745 (pmm) REVERT: D 18 ASP cc_start: 0.7043 (t0) cc_final: 0.6708 (t0) REVERT: D 32 ASN cc_start: 0.6607 (m-40) cc_final: 0.6256 (m-40) REVERT: D 208 LYS cc_start: 0.6427 (mmtt) cc_final: 0.5500 (mmtm) REVERT: E 55 SER cc_start: 0.8690 (p) cc_final: 0.8295 (p) REVERT: J 60 ASP cc_start: 0.7883 (p0) cc_final: 0.7541 (t0) REVERT: J 74 TYR cc_start: 0.6514 (m-10) cc_final: 0.6079 (m-10) REVERT: J 120 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7605 (mtm-85) REVERT: K 40 LYS cc_start: 0.6544 (mttt) cc_final: 0.4982 (mttt) REVERT: N 98 LEU cc_start: 0.9124 (tp) cc_final: 0.8713 (mt) REVERT: P 40 GLN cc_start: 0.4614 (mm-40) cc_final: 0.4331 (mm-40) REVERT: Q 54 ARG cc_start: 0.9088 (mtt-85) cc_final: 0.8740 (ttm-80) REVERT: R 1 MET cc_start: 0.4617 (tpt) cc_final: 0.4113 (ptp) REVERT: R 91 GLN cc_start: 0.8663 (tp40) cc_final: 0.7959 (tp-100) REVERT: R 99 THR cc_start: 0.7137 (p) cc_final: 0.6698 (p) REVERT: S 24 ILE cc_start: 0.8672 (pt) cc_final: 0.8450 (pt) REVERT: S 30 SER cc_start: 0.8669 (p) cc_final: 0.8128 (t) REVERT: S 78 GLU cc_start: 0.6490 (pt0) cc_final: 0.6254 (pt0) REVERT: T 5 GLU cc_start: 0.7501 (mp0) cc_final: 0.6355 (tm-30) REVERT: U 30 SER cc_start: 0.8849 (p) cc_final: 0.8637 (p) REVERT: X 35 HIS cc_start: 0.6634 (t-90) cc_final: 0.6213 (t-90) REVERT: 2 3 ARG cc_start: 0.7517 (mmt180) cc_final: 0.7064 (mmt180) REVERT: 2 15 SER cc_start: 0.7328 (p) cc_final: 0.6979 (p) REVERT: W 20 LYS cc_start: 0.8013 (ptpp) cc_final: 0.7624 (mttm) REVERT: W 79 GLU cc_start: 0.5763 (mt-10) cc_final: 0.5436 (mt-10) outliers start: 1 outliers final: 1 residues processed: 622 average time/residue: 0.8927 time to fit residues: 942.8928 Evaluate side-chains 483 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 482 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 176 optimal weight: 20.0000 chunk 472 optimal weight: 30.0000 chunk 103 optimal weight: 10.0000 chunk 308 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 525 optimal weight: 30.0000 chunk 436 optimal weight: 10.0000 chunk 243 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 275 optimal weight: 9.9990 overall best weight: 9.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN G 72 ASN ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN Q 80 ASN ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 GLN Z 8 GLN Z 33 HIS Z 48 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.6673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 87429 Z= 0.420 Angle : 0.874 14.519 131482 Z= 0.442 Chirality : 0.045 0.320 16887 Planarity : 0.007 0.080 6592 Dihedral : 24.065 179.905 45294 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 25.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.12 % Favored : 88.63 % Rotamer: Outliers : 0.04 % Allowed : 3.88 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.14), residues: 2788 helix: -1.42 (0.18), residues: 709 sheet: -1.13 (0.23), residues: 513 loop : -2.27 (0.14), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.004 TRP C 212 HIS 0.022 0.003 HIS J 80 PHE 0.031 0.003 PHE D 118 TYR 0.033 0.003 TYR C 95 ARG 0.070 0.001 ARG S 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 589 time to evaluate : 3.223 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: V 1 MET cc_start: 0.5708 (pmm) cc_final: 0.5292 (pmm) REVERT: C 63 ILE cc_start: 0.8750 (mm) cc_final: 0.8357 (mt) REVERT: D 126 ASN cc_start: 0.8016 (t0) cc_final: 0.7754 (t0) REVERT: E 55 SER cc_start: 0.8695 (p) cc_final: 0.8287 (p) REVERT: J 60 ASP cc_start: 0.8088 (p0) cc_final: 0.7854 (t0) REVERT: J 74 TYR cc_start: 0.7254 (m-10) cc_final: 0.7052 (m-80) REVERT: J 131 ASN cc_start: 0.6620 (p0) cc_final: 0.6234 (p0) REVERT: N 49 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7368 (mt-10) REVERT: N 56 LYS cc_start: 0.8349 (mtpt) cc_final: 0.8036 (mtpp) REVERT: P 36 LYS cc_start: 0.4816 (mppt) cc_final: 0.4558 (mptt) REVERT: Q 54 ARG cc_start: 0.9044 (mtt-85) cc_final: 0.8680 (ttm-80) REVERT: R 40 MET cc_start: 0.7301 (mmm) cc_final: 0.7058 (mmm) REVERT: R 91 GLN cc_start: 0.8879 (tp40) cc_final: 0.7942 (tp-100) REVERT: S 30 SER cc_start: 0.8735 (p) cc_final: 0.7572 (t) REVERT: T 5 GLU cc_start: 0.7675 (mp0) cc_final: 0.6361 (tm-30) REVERT: T 87 LEU cc_start: 0.7509 (mt) cc_final: 0.7259 (mt) REVERT: U 40 LEU cc_start: 0.7885 (mm) cc_final: 0.7417 (mm) REVERT: 2 31 LEU cc_start: 0.8929 (mm) cc_final: 0.8672 (mm) REVERT: O 76 LYS cc_start: 0.7984 (mttt) cc_final: 0.7267 (mttp) REVERT: O 89 ASP cc_start: 0.6769 (m-30) cc_final: 0.6298 (t0) outliers start: 1 outliers final: 0 residues processed: 590 average time/residue: 0.7762 time to fit residues: 780.3605 Evaluate side-chains 476 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 476 time to evaluate : 4.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 506 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 299 optimal weight: 3.9990 chunk 383 optimal weight: 0.8980 chunk 297 optimal weight: 6.9990 chunk 442 optimal weight: 7.9990 chunk 293 optimal weight: 4.9990 chunk 523 optimal weight: 20.0000 chunk 327 optimal weight: 30.0000 chunk 319 optimal weight: 20.0000 chunk 241 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 HIS ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN Q 13 HIS ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 87429 Z= 0.236 Angle : 0.668 12.507 131482 Z= 0.345 Chirality : 0.038 0.270 16887 Planarity : 0.005 0.080 6592 Dihedral : 23.854 179.858 45294 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.33 % Favored : 90.53 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.15), residues: 2788 helix: -0.98 (0.19), residues: 713 sheet: -0.99 (0.23), residues: 506 loop : -2.19 (0.14), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP C 212 HIS 0.017 0.002 HIS J 80 PHE 0.028 0.002 PHE Q 56 TYR 0.025 0.002 TYR F 21 ARG 0.011 0.001 ARG X 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 606 time to evaluate : 3.214 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: V 1 MET cc_start: 0.5529 (pmm) cc_final: 0.5125 (pmm) REVERT: D 1 MET cc_start: 0.7912 (tmm) cc_final: 0.7489 (tmm) REVERT: D 126 ASN cc_start: 0.7886 (t0) cc_final: 0.7681 (t0) REVERT: E 55 SER cc_start: 0.8692 (p) cc_final: 0.8260 (p) REVERT: J 60 ASP cc_start: 0.7959 (p0) cc_final: 0.7665 (t0) REVERT: J 74 TYR cc_start: 0.7159 (m-10) cc_final: 0.6749 (m-80) REVERT: J 131 ASN cc_start: 0.6331 (p0) cc_final: 0.6043 (p0) REVERT: K 58 LEU cc_start: 0.6501 (pp) cc_final: 0.6224 (pp) REVERT: L 55 MET cc_start: 0.4175 (tpt) cc_final: 0.3717 (tpt) REVERT: N 24 MET cc_start: 0.7919 (mtt) cc_final: 0.7696 (mtt) REVERT: P 10 GLU cc_start: 0.8491 (pm20) cc_final: 0.8085 (pm20) REVERT: P 32 VAL cc_start: 0.7085 (t) cc_final: 0.6698 (t) REVERT: P 36 LYS cc_start: 0.4163 (mppt) cc_final: 0.3773 (mptt) REVERT: P 63 ILE cc_start: 0.6554 (mm) cc_final: 0.6330 (mm) REVERT: Q 54 ARG cc_start: 0.9015 (mtt-85) cc_final: 0.8653 (ttm-80) REVERT: R 39 LEU cc_start: 0.7489 (mp) cc_final: 0.7260 (mp) REVERT: R 91 GLN cc_start: 0.8801 (tp40) cc_final: 0.7984 (tp-100) REVERT: S 30 SER cc_start: 0.8604 (p) cc_final: 0.7955 (t) REVERT: S 84 ARG cc_start: 0.8507 (mmp80) cc_final: 0.8240 (mmp80) REVERT: T 5 GLU cc_start: 0.7404 (mp0) cc_final: 0.6140 (tm-30) REVERT: T 87 LEU cc_start: 0.7125 (mt) cc_final: 0.6895 (mt) REVERT: X 24 THR cc_start: 0.5804 (m) cc_final: 0.5342 (m) REVERT: 2 15 SER cc_start: 0.7384 (p) cc_final: 0.7035 (p) REVERT: O 48 LEU cc_start: 0.4853 (mm) cc_final: 0.4409 (mm) REVERT: O 76 LYS cc_start: 0.7962 (mttt) cc_final: 0.7517 (mttp) outliers start: 0 outliers final: 0 residues processed: 606 average time/residue: 0.7808 time to fit residues: 803.4363 Evaluate side-chains 479 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 323 optimal weight: 5.9990 chunk 209 optimal weight: 50.0000 chunk 312 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 chunk 356 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 411 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 46 GLN G 37 ASN G 72 ASN G 127 GLN ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 ASN R 12 HIS ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 HIS Z 48 ASN W 36 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.7426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 87429 Z= 0.368 Angle : 0.820 12.438 131482 Z= 0.417 Chirality : 0.044 0.302 16887 Planarity : 0.007 0.114 6592 Dihedral : 24.096 179.673 45294 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.02 % Favored : 87.84 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.14), residues: 2788 helix: -1.30 (0.18), residues: 706 sheet: -1.16 (0.22), residues: 505 loop : -2.30 (0.14), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP C 212 HIS 0.022 0.003 HIS P 76 PHE 0.025 0.003 PHE Q 56 TYR 0.022 0.003 TYR C 95 ARG 0.034 0.001 ARG P 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 587 time to evaluate : 3.237 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: V 1 MET cc_start: 0.5849 (pmm) cc_final: 0.5451 (pmm) REVERT: D 1 MET cc_start: 0.7831 (tmm) cc_final: 0.7245 (tmm) REVERT: D 168 GLU cc_start: 0.7102 (tp30) cc_final: 0.6592 (tp30) REVERT: J 60 ASP cc_start: 0.8097 (p0) cc_final: 0.7797 (t0) REVERT: J 74 TYR cc_start: 0.7548 (m-10) cc_final: 0.7229 (m-80) REVERT: K 1 MET cc_start: 0.7419 (mmm) cc_final: 0.7194 (mmm) REVERT: K 58 LEU cc_start: 0.6756 (pp) cc_final: 0.6471 (pp) REVERT: N 56 LYS cc_start: 0.8316 (mtpt) cc_final: 0.7954 (mtpp) REVERT: Q 47 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7348 (ttp-170) REVERT: Q 54 ARG cc_start: 0.8949 (mtt-85) cc_final: 0.8688 (ttm-80) REVERT: Q 82 LEU cc_start: 0.7413 (mt) cc_final: 0.7210 (mt) REVERT: R 91 GLN cc_start: 0.8904 (tp40) cc_final: 0.8135 (tp-100) REVERT: S 30 SER cc_start: 0.8579 (p) cc_final: 0.7343 (t) REVERT: S 84 ARG cc_start: 0.8678 (mmp80) cc_final: 0.8386 (mmp80) REVERT: T 5 GLU cc_start: 0.7574 (mp0) cc_final: 0.6285 (tm-30) REVERT: T 87 LEU cc_start: 0.7352 (mt) cc_final: 0.7061 (mt) REVERT: X 26 ARG cc_start: 0.6550 (tpp80) cc_final: 0.6258 (tpp80) REVERT: 0 5 ASN cc_start: 0.8145 (m-40) cc_final: 0.6891 (t0) REVERT: 2 15 SER cc_start: 0.7476 (p) cc_final: 0.7110 (p) REVERT: 2 31 LEU cc_start: 0.8970 (mm) cc_final: 0.8683 (mm) REVERT: O 26 LEU cc_start: 0.6482 (tp) cc_final: 0.6276 (tp) REVERT: O 76 LYS cc_start: 0.8193 (mttt) cc_final: 0.7849 (mttt) REVERT: O 89 ASP cc_start: 0.6934 (m-30) cc_final: 0.6141 (t0) REVERT: F 120 SER cc_start: 0.5579 (p) cc_final: 0.3999 (p) REVERT: W 79 GLU cc_start: 0.6564 (mp0) cc_final: 0.5943 (mp0) outliers start: 0 outliers final: 0 residues processed: 587 average time/residue: 0.8123 time to fit residues: 815.0367 Evaluate side-chains 481 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 476 optimal weight: 8.9990 chunk 501 optimal weight: 20.0000 chunk 457 optimal weight: 5.9990 chunk 487 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 212 optimal weight: 30.0000 chunk 382 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 440 optimal weight: 0.9990 chunk 461 optimal weight: 10.0000 chunk 486 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN E 46 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN G 72 ASN J 76 HIS ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.7486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 87429 Z= 0.251 Angle : 0.687 12.447 131482 Z= 0.354 Chirality : 0.039 0.272 16887 Planarity : 0.005 0.098 6592 Dihedral : 23.950 179.882 45294 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.90 % Favored : 89.96 % Rotamer: Outliers : 0.09 % Allowed : 1.13 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.15), residues: 2788 helix: -1.05 (0.19), residues: 709 sheet: -1.18 (0.22), residues: 511 loop : -2.18 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP C 212 HIS 0.015 0.002 HIS J 80 PHE 0.021 0.002 PHE W 41 TYR 0.016 0.002 TYR N 112 ARG 0.008 0.001 ARG Z 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 586 time to evaluate : 3.264 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: D 1 MET cc_start: 0.7816 (tmm) cc_final: 0.7248 (tmm) REVERT: J 60 ASP cc_start: 0.8061 (p0) cc_final: 0.7722 (t0) REVERT: J 74 TYR cc_start: 0.7133 (m-10) cc_final: 0.6885 (m-80) REVERT: L 55 MET cc_start: 0.4465 (tpt) cc_final: 0.4111 (tpt) REVERT: N 98 LEU cc_start: 0.8937 (tt) cc_final: 0.8679 (mt) REVERT: P 10 GLU cc_start: 0.8486 (pm20) cc_final: 0.8266 (pm20) REVERT: P 63 ILE cc_start: 0.6899 (mm) cc_final: 0.6557 (mm) REVERT: Q 47 ARG cc_start: 0.7563 (ttp80) cc_final: 0.7108 (ttp-170) REVERT: Q 54 ARG cc_start: 0.9015 (mtt-85) cc_final: 0.8763 (ttm170) REVERT: R 25 LEU cc_start: 0.8709 (pp) cc_final: 0.8423 (pp) REVERT: R 60 LYS cc_start: 0.7028 (tppp) cc_final: 0.6706 (tppt) REVERT: R 91 GLN cc_start: 0.8844 (tp40) cc_final: 0.8054 (tp-100) REVERT: S 30 SER cc_start: 0.8491 (p) cc_final: 0.6867 (t) REVERT: S 84 ARG cc_start: 0.8550 (mmp80) cc_final: 0.8320 (mmp80) REVERT: T 5 GLU cc_start: 0.7587 (mp0) cc_final: 0.6340 (tm-30) REVERT: T 87 LEU cc_start: 0.7287 (mt) cc_final: 0.7085 (mt) REVERT: 0 5 ASN cc_start: 0.7932 (m-40) cc_final: 0.7070 (t0) REVERT: 2 15 SER cc_start: 0.7410 (p) cc_final: 0.7116 (p) REVERT: 2 31 LEU cc_start: 0.8958 (mm) cc_final: 0.8726 (mm) REVERT: O 26 LEU cc_start: 0.6413 (tp) cc_final: 0.6212 (tp) REVERT: O 76 LYS cc_start: 0.8107 (mttt) cc_final: 0.7820 (mttt) REVERT: O 89 ASP cc_start: 0.6605 (m-30) cc_final: 0.5922 (t0) outliers start: 2 outliers final: 1 residues processed: 588 average time/residue: 0.7834 time to fit residues: 784.6124 Evaluate side-chains 481 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 480 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 320 optimal weight: 0.7980 chunk 515 optimal weight: 30.0000 chunk 314 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 chunk 358 optimal weight: 7.9990 chunk 540 optimal weight: 8.9990 chunk 497 optimal weight: 5.9990 chunk 430 optimal weight: 1.9990 chunk 44 optimal weight: 30.0000 chunk 332 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN J 76 HIS ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN Z 48 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.7643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 87429 Z= 0.219 Angle : 0.652 12.109 131482 Z= 0.336 Chirality : 0.037 0.256 16887 Planarity : 0.005 0.083 6592 Dihedral : 23.871 179.222 45294 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.47 % Favored : 89.35 % Rotamer: Outliers : 0.04 % Allowed : 0.65 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.15), residues: 2788 helix: -0.88 (0.19), residues: 706 sheet: -1.22 (0.22), residues: 512 loop : -2.09 (0.14), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP C 212 HIS 0.013 0.002 HIS J 80 PHE 0.016 0.002 PHE U 72 TYR 0.023 0.002 TYR K 32 ARG 0.014 0.001 ARG T 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 582 time to evaluate : 3.248 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: C 63 ILE cc_start: 0.9127 (tp) cc_final: 0.8907 (tp) REVERT: C 224 MET cc_start: 0.6702 (mtp) cc_final: 0.6375 (mtp) REVERT: D 1 MET cc_start: 0.7758 (tmm) cc_final: 0.7259 (tmm) REVERT: D 167 ASN cc_start: 0.5630 (t0) cc_final: 0.5406 (t0) REVERT: D 168 GLU cc_start: 0.6915 (tp30) cc_final: 0.6712 (tp30) REVERT: J 60 ASP cc_start: 0.8090 (p0) cc_final: 0.7598 (t0) REVERT: J 74 TYR cc_start: 0.7347 (m-10) cc_final: 0.6972 (m-80) REVERT: K 58 LEU cc_start: 0.6597 (pp) cc_final: 0.6231 (pp) REVERT: L 55 MET cc_start: 0.4588 (tpt) cc_final: 0.4233 (tpt) REVERT: N 24 MET cc_start: 0.7900 (mtt) cc_final: 0.7482 (mtt) REVERT: N 98 LEU cc_start: 0.8968 (tt) cc_final: 0.8716 (mt) REVERT: Q 47 ARG cc_start: 0.7515 (ttp80) cc_final: 0.7082 (ttp-170) REVERT: Q 54 ARG cc_start: 0.8948 (mtt-85) cc_final: 0.8637 (ttm-80) REVERT: R 25 LEU cc_start: 0.8764 (pp) cc_final: 0.8401 (pp) REVERT: R 86 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8936 (pp30) REVERT: R 91 GLN cc_start: 0.8845 (tp40) cc_final: 0.8075 (tp-100) REVERT: R 99 THR cc_start: 0.7014 (p) cc_final: 0.6575 (p) REVERT: S 2 GLU cc_start: 0.7071 (mp0) cc_final: 0.6299 (pp20) REVERT: S 30 SER cc_start: 0.8353 (p) cc_final: 0.6772 (t) REVERT: S 65 ASP cc_start: 0.7294 (t0) cc_final: 0.7076 (t0) REVERT: S 84 ARG cc_start: 0.8492 (mmp80) cc_final: 0.8261 (mmp80) REVERT: T 5 GLU cc_start: 0.7607 (mp0) cc_final: 0.6504 (tm-30) REVERT: T 87 LEU cc_start: 0.7142 (mt) cc_final: 0.6908 (mt) REVERT: X 26 ARG cc_start: 0.6363 (tpp80) cc_final: 0.6069 (tpp80) REVERT: X 35 HIS cc_start: 0.6409 (t-90) cc_final: 0.5974 (t-90) REVERT: Y 29 ARG cc_start: 0.6848 (ptm160) cc_final: 0.6604 (ptm-80) REVERT: 0 5 ASN cc_start: 0.7841 (m-40) cc_final: 0.7292 (t0) REVERT: 2 15 SER cc_start: 0.7342 (p) cc_final: 0.7038 (p) REVERT: 2 31 LEU cc_start: 0.8933 (mm) cc_final: 0.8730 (mm) REVERT: O 89 ASP cc_start: 0.6432 (m-30) cc_final: 0.5786 (t0) REVERT: F 120 SER cc_start: 0.7026 (m) cc_final: 0.6496 (m) REVERT: W 15 LYS cc_start: 0.5746 (mtpt) cc_final: 0.5488 (mtpt) REVERT: W 79 GLU cc_start: 0.6820 (mp0) cc_final: 0.6051 (mp0) outliers start: 1 outliers final: 0 residues processed: 583 average time/residue: 0.7836 time to fit residues: 779.5542 Evaluate side-chains 479 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 478 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 342 optimal weight: 0.9990 chunk 458 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 397 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 431 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 chunk 443 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 overall best weight: 4.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.114882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.087254 restraints weight = 251917.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.089978 restraints weight = 106730.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.091013 restraints weight = 58237.615| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.7853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 87429 Z= 0.242 Angle : 0.672 12.064 131482 Z= 0.345 Chirality : 0.038 0.307 16887 Planarity : 0.005 0.083 6592 Dihedral : 23.889 179.597 45294 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.11 % Favored : 89.74 % Rotamer: Outliers : 0.09 % Allowed : 0.57 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 3.49 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.15), residues: 2788 helix: -0.91 (0.19), residues: 692 sheet: -1.14 (0.23), residues: 493 loop : -2.09 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 212 HIS 0.011 0.002 HIS J 80 PHE 0.040 0.002 PHE Q 56 TYR 0.019 0.002 TYR 0 47 ARG 0.025 0.001 ARG T 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14586.00 seconds wall clock time: 257 minutes 33.20 seconds (15453.20 seconds total)