Starting phenix.real_space_refine on Mon Sep 30 09:53:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqq_21873/09_2024/6wqq_21873.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqq_21873/09_2024/6wqq_21873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqq_21873/09_2024/6wqq_21873.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqq_21873/09_2024/6wqq_21873.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqq_21873/09_2024/6wqq_21873.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqq_21873/09_2024/6wqq_21873.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 6 Type Number sf(0) Gaussians P 2803 5.49 5 S 56 5.16 5 C 39961 2.51 5 N 15060 2.21 5 O 23253 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 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: 81134 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 915 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "B" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2094 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Chain: "C" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "D" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 785 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 97} Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 106} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 711 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "G" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 770 Classifications: {'peptide': 100} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 727 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "J" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 463 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "K" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 495 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Chain: "M" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 432 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "N" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 397 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "O" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 390 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "P" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "Q" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "R" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "S" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1472 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain: "V" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1138 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "W" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 911 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "X" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1082 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "Y" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1089 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "Z" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 955 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain: "a" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'TRANS': 108} Chain breaks: 1 Chain: "1" Number of atoms: 57851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2698, 57851 Inner-chain residues flagged as termini: ['pdbres=" A 1 318 "', 'pdbres=" A 11459 "', 'pdbres=" U 11540 "', 'pdbres=" G 11556 "'] Classifications: {'RNA': 2698} Modifications used: {'5*END': 5, 'rna2p_pur': 272, 'rna2p_pyr': 136, 'rna3p_pur': 1281, 'rna3p_pyr': 1009} Link IDs: {'rna2p': 408, 'rna3p': 2289} Chain breaks: 6 Chain: "2" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 2358 Classifications: {'RNA': 111} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 50, 'rna3p_pyr': 49} Link IDs: {'rna2p': 12, 'rna3p': 98} Chain: "I" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 597 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "1" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'RD8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 34.67, per 1000 atoms: 0.43 Number of scatterers: 81134 At special positions: 0 Unit cell: (212.04, 234.84, 188.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 2803 15.00 F 1 9.00 O 23253 8.00 N 15060 7.00 C 39961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 43 " distance=2.04 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS R 27 " distance=2.04 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: 14.47 Conformation dependent library (CDL) restraints added in 3.4 seconds 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4856 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 39 sheets defined 24.9% alpha, 19.8% beta 540 base pairs and 1570 stacking pairs defined. Time for finding SS restraints: 27.97 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.617A pdb=" N GLU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 9 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.732A pdb=" N LEU A 102 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 103 " --> pdb=" O TYR A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 103' Processing helix chain 'A' and resid 106 through 110 removed outlier: 3.878A pdb=" N ALA A 109 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.507A pdb=" N HIS B 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU B 201 " --> pdb=" O LEU B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 197 through 201' Processing helix chain 'B' and resid 207 through 213 removed outlier: 4.037A pdb=" N SER B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 265 through 268 removed outlier: 3.804A pdb=" N LYS B 268 " --> pdb=" O SER B 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 265 through 268' Processing helix chain 'C' and resid 9 through 21 removed outlier: 3.916A pdb=" N ARG C 13 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 31 through 70 removed outlier: 3.905A pdb=" N GLN C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG C 55 " --> pdb=" O ARG C 51 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG C 58 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 75 through 86 removed outlier: 3.662A pdb=" N ASN C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY C 82 " --> pdb=" O ARG C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.601A pdb=" N GLU C 97 " --> pdb=" O LYS C 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 removed outlier: 3.828A pdb=" N PHE C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN C 108 " --> pdb=" O LYS C 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 25 removed outlier: 3.534A pdb=" N VAL E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE E 24 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 38 removed outlier: 3.755A pdb=" N ILE E 33 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 61 removed outlier: 3.515A pdb=" N LEU E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 69 removed outlier: 4.016A pdb=" N GLU E 68 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU E 69 " --> pdb=" O THR E 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 65 through 69' Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'F' and resid 34 through 47 removed outlier: 3.549A pdb=" N MET F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 25 removed outlier: 3.759A pdb=" N GLY H 25 " --> pdb=" O LEU H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 56 removed outlier: 3.598A pdb=" N LYS H 50 " --> pdb=" O VAL H 46 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL H 51 " --> pdb=" O GLU H 47 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG H 53 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 84 removed outlier: 3.729A pdb=" N ASN H 84 " --> pdb=" O PRO H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'J' and resid 51 through 55 Processing helix chain 'K' and resid 12 through 22 removed outlier: 3.521A pdb=" N SER K 21 " --> pdb=" O GLN K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 34 removed outlier: 3.613A pdb=" N ARG K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE K 30 " --> pdb=" O PHE K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 61 removed outlier: 3.660A pdb=" N THR K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU K 61 " --> pdb=" O ALA K 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 75 Processing helix chain 'L' and resid 106 through 111 removed outlier: 3.896A pdb=" N THR L 109 " --> pdb=" O SER L 106 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL L 111 " --> pdb=" O ASP L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 135 Processing helix chain 'M' and resid 16 through 25 removed outlier: 3.764A pdb=" N THR M 22 " --> pdb=" O THR M 18 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL M 23 " --> pdb=" O GLN M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 48 removed outlier: 3.707A pdb=" N GLN M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE M 47 " --> pdb=" O ILE M 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 17 removed outlier: 3.620A pdb=" N ARG N 17 " --> pdb=" O LYS N 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 15 Processing helix chain 'P' and resid 18 through 23 Processing helix chain 'P' and resid 25 through 39 removed outlier: 3.629A pdb=" N VAL P 31 " --> pdb=" O ASN P 27 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU P 32 " --> pdb=" O GLY P 28 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA P 33 " --> pdb=" O ARG P 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 12 removed outlier: 3.717A pdb=" N LYS Q 12 " --> pdb=" O ARG Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 43 Processing helix chain 'Q' and resid 51 through 58 removed outlier: 3.686A pdb=" N LYS Q 56 " --> pdb=" O LYS Q 52 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG Q 57 " --> pdb=" O SER Q 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 42 removed outlier: 3.616A pdb=" N GLU S 35 " --> pdb=" O SER S 31 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE S 37 " --> pdb=" O LEU S 33 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN S 40 " --> pdb=" O ALA S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 120 removed outlier: 3.996A pdb=" N LEU S 108 " --> pdb=" O LYS S 104 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL S 118 " --> pdb=" O LEU S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 146 removed outlier: 3.890A pdb=" N ASN S 141 " --> pdb=" O LYS S 137 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL S 142 " --> pdb=" O GLU S 138 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU S 143 " --> pdb=" O PHE S 139 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 189 removed outlier: 3.521A pdb=" N ASN S 188 " --> pdb=" O LEU S 184 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA S 189 " --> pdb=" O ASP S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 196 through 206 removed outlier: 3.831A pdb=" N GLU S 204 " --> pdb=" O LYS S 200 " (cutoff:3.500A) Processing helix chain 'V' and resid 25 through 39 removed outlier: 3.551A pdb=" N SER V 31 " --> pdb=" O GLY V 27 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU V 32 " --> pdb=" O ARG V 28 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 73 removed outlier: 3.650A pdb=" N LYS V 73 " --> pdb=" O LYS V 69 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 97 removed outlier: 3.631A pdb=" N ARG V 95 " --> pdb=" O GLY V 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 108 removed outlier: 3.628A pdb=" N LEU V 101 " --> pdb=" O ASN V 97 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE V 102 " --> pdb=" O PRO V 98 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER V 105 " --> pdb=" O LEU V 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 119 removed outlier: 3.592A pdb=" N LYS V 118 " --> pdb=" O ARG V 114 " (cutoff:3.500A) Processing helix chain 'W' and resid 111 through 118 Processing helix chain 'X' and resid 37 through 41 removed outlier: 3.704A pdb=" N ARG X 41 " --> pdb=" O GLN X 38 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 60 removed outlier: 3.554A pdb=" N ARG X 59 " --> pdb=" O PRO X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 83 removed outlier: 3.879A pdb=" N LEU X 82 " --> pdb=" O ASN X 78 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN X 83 " --> pdb=" O LEU X 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 78 through 83' Processing helix chain 'X' and resid 92 through 99 removed outlier: 3.760A pdb=" N VAL X 97 " --> pdb=" O PRO X 93 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU X 98 " --> pdb=" O ALA X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 133 through 139 removed outlier: 3.790A pdb=" N ASP X 137 " --> pdb=" O ALA X 133 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS X 139 " --> pdb=" O ALA X 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 56 Processing helix chain 'Y' and resid 110 through 121 removed outlier: 3.592A pdb=" N ARG Y 115 " --> pdb=" O GLU Y 111 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU Y 116 " --> pdb=" O GLU Y 112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 27 removed outlier: 3.528A pdb=" N ASP Z 19 " --> pdb=" O ALA Z 15 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE Z 26 " --> pdb=" O THR Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 34 through 54 removed outlier: 3.845A pdb=" N GLU Z 39 " --> pdb=" O ALA Z 35 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER Z 42 " --> pdb=" O LYS Z 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL Z 43 " --> pdb=" O GLU Z 39 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU Z 45 " --> pdb=" O ARG Z 41 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR Z 49 " --> pdb=" O GLU Z 45 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU Z 50 " --> pdb=" O LYS Z 46 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS Z 53 " --> pdb=" O THR Z 49 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY Z 54 " --> pdb=" O LEU Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 62 Processing helix chain 'Z' and resid 81 through 85 removed outlier: 3.730A pdb=" N LEU Z 85 " --> pdb=" O ALA Z 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 81 through 85' Processing helix chain 'Z' and resid 87 through 93 removed outlier: 3.653A pdb=" N TYR Z 93 " --> pdb=" O ILE Z 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 23 removed outlier: 3.946A pdb=" N LYS a 13 " --> pdb=" O LYS a 9 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG a 14 " --> pdb=" O VAL a 10 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG a 17 " --> pdb=" O LYS a 13 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL a 18 " --> pdb=" O ARG a 14 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR a 20 " --> pdb=" O ALA a 16 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASN a 21 " --> pdb=" O ARG a 17 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU a 22 " --> pdb=" O VAL a 18 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER a 23 " --> pdb=" O ARG a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 87 removed outlier: 3.792A pdb=" N GLY a 77 " --> pdb=" O ALA a 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU a 78 " --> pdb=" O THR a 74 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS a 87 " --> pdb=" O LYS a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 115 removed outlier: 3.613A pdb=" N ALA a 112 " --> pdb=" O LEU a 108 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER a 115 " --> pdb=" O ALA a 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 90 removed outlier: 7.120A pdb=" N HIS A 31 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE A 86 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG A 29 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL A 88 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR A 27 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLU A 46 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ILE A 66 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR A 62 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ARG A 52 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR A 60 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AA3, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 105 removed outlier: 4.135A pdb=" N SER B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 95 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL B 78 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE B 74 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 129 through 131 removed outlier: 3.877A pdb=" N GLN B 163 " --> pdb=" O ARG B 175 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 173 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LYS B 167 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TYR B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET B 183 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 270 " --> pdb=" O MET B 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 144 through 145 removed outlier: 6.383A pdb=" N ILE B 144 " --> pdb=" O GLN B 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.505A pdb=" N ILE D 4 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 19 through 22 removed outlier: 3.745A pdb=" N LYS D 64 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR D 96 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL D 62 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASP D 98 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ALA D 60 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 77 removed outlier: 4.800A pdb=" N SER D 82 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 10 removed outlier: 3.913A pdb=" N THR E 9 " --> pdb=" O SER E 101 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER E 101 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N HIS E 102 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA E 76 " --> pdb=" O HIS E 102 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR E 104 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA E 74 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL E 106 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 82 through 87 Processing sheet with id=AB3, first strand: chain 'F' and resid 7 through 10 removed outlier: 6.568A pdb=" N ASP F 28 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR F 26 " --> pdb=" O PRO F 10 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG F 76 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARG F 75 " --> pdb=" O ASN F 57 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASN F 57 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS F 77 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE F 55 " --> pdb=" O LYS F 77 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE F 79 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL F 53 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR F 81 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LYS F 49 " --> pdb=" O LYS F 83 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 62 through 63 removed outlier: 3.514A pdb=" N LYS F 63 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY F 70 " --> pdb=" O LYS F 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 63 through 64 removed outlier: 3.652A pdb=" N ALA G 25 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASN G 8 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU G 71 " --> pdb=" O ASN G 8 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU G 70 " --> pdb=" O THR G 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 40 through 43 removed outlier: 3.787A pdb=" N THR G 59 " --> pdb=" O MET G 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 81 through 82 Processing sheet with id=AB8, first strand: chain 'H' and resid 7 through 8 removed outlier: 9.084A pdb=" N LYS H 26 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N ILE H 89 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE H 91 " --> pdb=" O PRO H 28 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL H 30 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ALA H 93 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN H 85 " --> pdb=" O ASP H 80 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN H 78 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE H 89 " --> pdb=" O ASP H 76 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP H 76 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE H 91 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL H 74 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA H 93 " --> pdb=" O VAL H 72 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL H 72 " --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 13 through 16 removed outlier: 3.519A pdb=" N ARG J 27 " --> pdb=" O GLY J 15 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 33 through 38 removed outlier: 3.587A pdb=" N VAL J 36 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 179 through 183 removed outlier: 5.738A pdb=" N GLN L 181 " --> pdb=" O VAL L 118 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL L 118 " --> pdb=" O GLN L 181 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU L 210 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LYS L 9 " --> pdb=" O GLU L 29 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU L 29 " --> pdb=" O LYS L 9 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY L 11 " --> pdb=" O VAL L 27 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL L 194 " --> pdb=" O VAL L 188 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL L 188 " --> pdb=" O VAL L 194 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU L 196 " --> pdb=" O VAL L 186 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 85 through 91 removed outlier: 3.681A pdb=" N GLU L 54 " --> pdb=" O ARG L 86 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE L 88 " --> pdb=" O GLY L 52 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY L 52 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU L 90 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLN L 50 " --> pdb=" O GLU L 90 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN L 37 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY L 52 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL L 35 " --> pdb=" O GLY L 52 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N GLU L 54 " --> pdb=" O ASN L 33 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N ASN L 33 " --> pdb=" O GLU L 54 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN L 33 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 34 through 37 removed outlier: 4.286A pdb=" N GLN M 5 " --> pdb=" O GLU M 57 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 27 through 29 Processing sheet with id=AC6, first strand: chain 'O' and resid 17 through 22 removed outlier: 3.558A pdb=" N THR O 19 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS O 21 " --> pdb=" O VAL O 3 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS O 41 " --> pdb=" O CYS O 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Q' and resid 14 through 16 Processing sheet with id=AC8, first strand: chain 'R' and resid 2 through 3 removed outlier: 6.458A pdb=" N LYS R 2 " --> pdb=" O ARG R 35 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 123 through 126 removed outlier: 6.187A pdb=" N LEU S 153 " --> pdb=" O VAL S 193 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR S 195 " --> pdb=" O LEU S 153 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL S 155 " --> pdb=" O THR S 195 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL S 152 " --> pdb=" O GLN S 174 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N THR S 176 " --> pdb=" O VAL S 152 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL S 154 " --> pdb=" O THR S 176 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 123 through 125 removed outlier: 6.701A pdb=" N TRP V 16 " --> pdb=" O GLU V 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 74 through 78 Processing sheet with id=AD3, first strand: chain 'W' and resid 7 through 10 removed outlier: 5.549A pdb=" N ARG W 17 " --> pdb=" O VAL W 10 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN W 45 " --> pdb=" O ARG W 17 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL W 19 " --> pdb=" O VAL W 43 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL W 43 " --> pdb=" O VAL W 19 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR W 21 " --> pdb=" O CYS W 41 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N CYS W 41 " --> pdb=" O THR W 21 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS W 23 " --> pdb=" O ILE W 39 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ILE W 39 " --> pdb=" O LYS W 23 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA W 83 " --> pdb=" O VAL W 63 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N CYS W 84 " --> pdb=" O ARG W 7 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS W 9 " --> pdb=" O CYS W 84 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE W 86 " --> pdb=" O LYS W 9 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 75 through 77 removed outlier: 6.077A pdb=" N ALA X 75 " --> pdb=" O LYS X 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'X' and resid 90 through 91 removed outlier: 6.385A pdb=" N VAL X 123 " --> pdb=" O GLU X 144 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 63 through 66 removed outlier: 4.265A pdb=" N PHE Y 104 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Y' and resid 40 through 43 removed outlier: 3.690A pdb=" N ILE Y 42 " --> pdb=" O ALA Y 95 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL Y 90 " --> pdb=" O LYS Y 76 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LYS Y 76 " --> pdb=" O VAL Y 90 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY Y 92 " --> pdb=" O TYR Y 74 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Z' and resid 29 through 33 removed outlier: 6.536A pdb=" N SER Z 116 " --> pdb=" O GLN Z 106 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 70 through 71 Processing sheet with id=AE1, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.785A pdb=" N ILE a 44 " --> pdb=" O LEU a 53 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLN a 55 " --> pdb=" O ALA a 42 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA a 42 " --> pdb=" O GLN a 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 30 through 31 removed outlier: 6.572A pdb=" N LEU I 67 " --> pdb=" O LEU I 45 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.573A pdb=" N GLY I 73 " --> pdb=" O VAL I 39 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1264 hydrogen bonds 2012 hydrogen bond angles 0 basepair planarities 540 basepair parallelities 1570 stacking parallelities Total time for adding SS restraints: 126.10 Time building geometry restraints manager: 17.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 7648 1.31 - 1.44: 40190 1.44 - 1.57: 35081 1.57 - 1.70: 5600 1.70 - 1.83: 98 Bond restraints: 88617 Sorted by residual: bond pdb=" C30 RD8 13001 " pdb=" O29 RD8 13001 " ideal model delta sigma weight residual 1.334 1.446 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C26 RD8 13001 " pdb=" N25 RD8 13001 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C30 RD8 13001 " pdb=" N21 RD8 13001 " ideal model delta sigma weight residual 1.368 1.465 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" N16 RD8 13001 " pdb=" N17 RD8 13001 " ideal model delta sigma weight residual 1.289 1.368 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" CG ASN K 8 " pdb=" ND2 ASN K 8 " ideal model delta sigma weight residual 1.328 1.249 0.079 2.10e-02 2.27e+03 1.41e+01 ... (remaining 88612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 132790 2.33 - 4.66: 601 4.66 - 6.99: 68 6.99 - 9.32: 15 9.32 - 11.65: 6 Bond angle restraints: 133480 Sorted by residual: angle pdb=" O3' G 12094 " pdb=" C3' G 12094 " pdb=" C2' G 12094 " ideal model delta sigma weight residual 109.50 97.85 11.65 1.50e+00 4.44e-01 6.03e+01 angle pdb=" C4' A 11866 " pdb=" C3' A 11866 " pdb=" O3' A 11866 " ideal model delta sigma weight residual 113.00 123.90 -10.90 1.50e+00 4.44e-01 5.28e+01 angle pdb=" O2' A 1 849 " pdb=" C2' A 1 849 " pdb=" C1' A 1 849 " ideal model delta sigma weight residual 108.40 97.63 10.77 1.50e+00 4.44e-01 5.15e+01 angle pdb=" C4' G 12657 " pdb=" C3' G 12657 " pdb=" O3' G 12657 " ideal model delta sigma weight residual 113.00 123.50 -10.50 1.50e+00 4.44e-01 4.90e+01 angle pdb=" N THR Z 77 " pdb=" CA THR Z 77 " pdb=" C THR Z 77 " ideal model delta sigma weight residual 112.24 120.60 -8.36 1.28e+00 6.10e-01 4.27e+01 ... (remaining 133475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 50125 35.97 - 71.95: 5777 71.95 - 107.92: 697 107.92 - 143.89: 14 143.89 - 179.87: 23 Dihedral angle restraints: 56636 sinusoidal: 49077 harmonic: 7559 Sorted by residual: dihedral pdb=" O4' C 2 79 " pdb=" C1' C 2 79 " pdb=" N1 C 2 79 " pdb=" C2 C 2 79 " ideal model delta sinusoidal sigma weight residual 200.00 20.13 179.87 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 12607 " pdb=" C1' U 12607 " pdb=" N1 U 12607 " pdb=" C2 U 12607 " ideal model delta sinusoidal sigma weight residual 200.00 21.21 178.79 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 12639 " pdb=" C1' C 12639 " pdb=" N1 C 12639 " pdb=" C2 C 12639 " ideal model delta sinusoidal sigma weight residual -160.00 12.53 -172.53 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 56633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 17071 0.113 - 0.227: 108 0.227 - 0.340: 17 0.340 - 0.453: 4 0.453 - 0.567: 2 Chirality restraints: 17202 Sorted by residual: chirality pdb=" CA THR Z 77 " pdb=" N THR Z 77 " pdb=" C THR Z 77 " pdb=" CB THR Z 77 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" CA HIS L 143 " pdb=" N HIS L 143 " pdb=" C HIS L 143 " pdb=" CB HIS L 143 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.16e+00 chirality pdb=" C3' G 12096 " pdb=" C4' G 12096 " pdb=" O3' G 12096 " pdb=" C2' G 12096 " both_signs ideal model delta sigma weight residual False -2.48 -2.04 -0.44 2.00e-01 2.50e+01 4.77e+00 ... (remaining 17199 not shown) Planarity restraints: 6446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 1 721 " -0.059 2.00e-02 2.50e+03 2.92e-02 2.35e+01 pdb=" N9 A 1 721 " 0.074 2.00e-02 2.50e+03 pdb=" C8 A 1 721 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A 1 721 " -0.007 2.00e-02 2.50e+03 pdb=" C5 A 1 721 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A 1 721 " -0.012 2.00e-02 2.50e+03 pdb=" N6 A 1 721 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A 1 721 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A 1 721 " 0.008 2.00e-02 2.50e+03 pdb=" N3 A 1 721 " 0.008 2.00e-02 2.50e+03 pdb=" C4 A 1 721 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11866 " -0.045 2.00e-02 2.50e+03 2.46e-02 1.66e+01 pdb=" N9 A 11866 " 0.067 2.00e-02 2.50e+03 pdb=" C8 A 11866 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A 11866 " -0.006 2.00e-02 2.50e+03 pdb=" C5 A 11866 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A 11866 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A 11866 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A 11866 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A 11866 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A 11866 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A 11866 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET L 141 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C MET L 141 " -0.061 2.00e-02 2.50e+03 pdb=" O MET L 141 " 0.023 2.00e-02 2.50e+03 pdb=" N SER L 142 " 0.021 2.00e-02 2.50e+03 ... (remaining 6443 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 9761 2.74 - 3.28: 65280 3.28 - 3.82: 149111 3.82 - 4.36: 206921 4.36 - 4.90: 272902 Nonbonded interactions: 703975 Sorted by model distance: nonbonded pdb=" O2' G 1 904 " pdb=" O6 G 1 961 " model vdw 2.203 3.040 nonbonded pdb=" OG SER a 36 " pdb=" O HIS a 39 " model vdw 2.209 3.040 nonbonded pdb=" OP2 U 11806 " pdb=" N6 A 11811 " model vdw 2.213 3.120 nonbonded pdb=" O2' U 12370 " pdb=" O2' U 12400 " model vdw 2.217 3.040 nonbonded pdb=" O2' A 12060 " pdb=" OP2 G 12062 " model vdw 2.219 3.040 ... (remaining 703970 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 2.610 Check model and map are aligned: 0.480 Set scattering table: 0.610 Process input model: 246.680 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.260 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 260.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.002 0.112 88617 Z= 0.128 Angle : 0.450 11.648 133480 Z= 0.279 Chirality : 0.029 0.567 17202 Planarity : 0.003 0.036 6446 Dihedral : 22.726 179.866 51774 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.36 % Allowed : 4.44 % Favored : 95.21 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.12), residues: 2619 helix: -4.26 (0.10), residues: 572 sheet: -1.50 (0.21), residues: 511 loop : -2.56 (0.12), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 213 HIS 0.003 0.001 HIS C 29 PHE 0.009 0.001 PHE K 30 TYR 0.009 0.001 TYR F 58 ARG 0.004 0.000 ARG N 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 463 time to evaluate : 3.346 Fit side-chains REVERT: A 87 GLU cc_start: 0.7468 (pt0) cc_final: 0.7197 (pt0) REVERT: A 91 ARG cc_start: 0.6370 (mtt90) cc_final: 0.6131 (mmt90) REVERT: A 108 LYS cc_start: 0.6186 (mtmm) cc_final: 0.4920 (mtmm) REVERT: B 132 LEU cc_start: 0.7999 (mt) cc_final: 0.7759 (mt) REVERT: F 65 MET cc_start: 0.4711 (mtp) cc_final: 0.4299 (tmm) REVERT: J 3 LYS cc_start: 0.7204 (pttm) cc_final: 0.6959 (ptmt) REVERT: L 61 LYS cc_start: 0.5547 (tptt) cc_final: 0.5284 (mttm) REVERT: N 14 ASN cc_start: 0.8676 (m-40) cc_final: 0.8472 (m-40) REVERT: O 46 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7813 (ttm-80) REVERT: R 24 MET cc_start: 0.7798 (mmm) cc_final: 0.7594 (mmm) REVERT: S 201 LYS cc_start: 0.7954 (tptm) cc_final: 0.7704 (tttt) REVERT: S 204 GLU cc_start: 0.6582 (pp20) cc_final: 0.6114 (pp20) REVERT: V 88 ILE cc_start: 0.8087 (mp) cc_final: 0.7769 (mt) REVERT: V 121 LYS cc_start: 0.7979 (mttm) cc_final: 0.7651 (mttp) REVERT: Z 19 ASP cc_start: 0.5446 (m-30) cc_final: 0.5224 (m-30) REVERT: Z 53 LYS cc_start: 0.7114 (mmtt) cc_final: 0.6882 (mmtp) REVERT: Z 71 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7055 (mt) REVERT: a 43 GLN cc_start: 0.7546 (pt0) cc_final: 0.7323 (pt0) outliers start: 8 outliers final: 3 residues processed: 470 average time/residue: 0.9178 time to fit residues: 706.9641 Evaluate side-chains 363 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 359 time to evaluate : 3.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 79 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 538 random chunks: chunk 454 optimal weight: 6.9990 chunk 407 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 chunk 275 optimal weight: 6.9990 chunk 217 optimal weight: 0.0980 chunk 421 optimal weight: 5.9990 chunk 163 optimal weight: 0.0070 chunk 256 optimal weight: 7.9990 chunk 313 optimal weight: 6.9990 chunk 488 optimal weight: 7.9990 overall best weight: 2.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN C 108 GLN E 61 ASN G 69 GLN H 13 GLN L 143 HIS X 27 ASN Y 12 GLN Z 79 GLN Z 97 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 88617 Z= 0.272 Angle : 0.673 9.770 133480 Z= 0.341 Chirality : 0.040 0.336 17202 Planarity : 0.005 0.078 6446 Dihedral : 23.250 179.309 46385 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.37 % Allowed : 13.31 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.14), residues: 2619 helix: -2.61 (0.17), residues: 612 sheet: -1.10 (0.21), residues: 535 loop : -2.18 (0.13), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 213 HIS 0.008 0.001 HIS Q 31 PHE 0.016 0.002 PHE S 139 TYR 0.019 0.002 TYR H 32 ARG 0.007 0.001 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 359 time to evaluate : 3.346 Fit side-chains REVERT: A 87 GLU cc_start: 0.7422 (pt0) cc_final: 0.7206 (pt0) REVERT: A 91 ARG cc_start: 0.6601 (mtt90) cc_final: 0.6380 (mmt90) REVERT: A 108 LYS cc_start: 0.6254 (mtmm) cc_final: 0.5020 (mtmm) REVERT: F 25 TYR cc_start: 0.7787 (m-80) cc_final: 0.7365 (m-80) REVERT: J 3 LYS cc_start: 0.7259 (pttm) cc_final: 0.6955 (ptmt) REVERT: O 4 ASN cc_start: 0.6634 (m-40) cc_final: 0.6402 (m110) REVERT: S 201 LYS cc_start: 0.7845 (tptm) cc_final: 0.7386 (tptt) REVERT: S 204 GLU cc_start: 0.6445 (pp20) cc_final: 0.6084 (pp20) REVERT: V 46 THR cc_start: 0.7992 (t) cc_final: 0.7444 (m) REVERT: V 88 ILE cc_start: 0.8105 (mp) cc_final: 0.7803 (mt) REVERT: W 114 ILE cc_start: 0.8082 (mm) cc_final: 0.7826 (mm) REVERT: Z 19 ASP cc_start: 0.5238 (m-30) cc_final: 0.4942 (m-30) REVERT: Z 53 LYS cc_start: 0.7120 (mmtt) cc_final: 0.6699 (mmtp) outliers start: 53 outliers final: 41 residues processed: 393 average time/residue: 0.8321 time to fit residues: 548.1613 Evaluate side-chains 377 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 336 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 164 GLU Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 77 ILE Chi-restraints excluded: chain X residue 27 ASN Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 538 random chunks: chunk 271 optimal weight: 6.9990 chunk 151 optimal weight: 0.6980 chunk 406 optimal weight: 6.9990 chunk 332 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 489 optimal weight: 6.9990 chunk 528 optimal weight: 8.9990 chunk 435 optimal weight: 6.9990 chunk 485 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 392 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN B 194 GLN F 69 GLN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 GLN ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN Z 97 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 88617 Z= 0.384 Angle : 0.808 11.065 133480 Z= 0.403 Chirality : 0.046 0.367 17202 Planarity : 0.006 0.096 6446 Dihedral : 23.609 179.331 46379 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.08 % Allowed : 15.82 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.14), residues: 2619 helix: -2.22 (0.18), residues: 628 sheet: -1.26 (0.21), residues: 571 loop : -2.15 (0.14), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 213 HIS 0.007 0.002 HIS B 230 PHE 0.020 0.003 PHE S 129 TYR 0.018 0.003 TYR V 45 ARG 0.009 0.001 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 338 time to evaluate : 3.332 Fit side-chains REVERT: A 87 GLU cc_start: 0.7331 (pt0) cc_final: 0.7111 (pt0) REVERT: A 108 LYS cc_start: 0.6355 (mtmm) cc_final: 0.5026 (mtmm) REVERT: C 74 MET cc_start: 0.6035 (ptm) cc_final: 0.5832 (ptm) REVERT: E 31 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6638 (tp30) REVERT: F 25 TYR cc_start: 0.7895 (m-80) cc_final: 0.7648 (m-80) REVERT: M 6 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7564 (mp) REVERT: O 1 MET cc_start: 0.5448 (OUTLIER) cc_final: 0.5069 (mmt) REVERT: S 201 LYS cc_start: 0.7881 (tptm) cc_final: 0.7395 (tptt) REVERT: S 204 GLU cc_start: 0.6671 (pp20) cc_final: 0.6300 (pp20) REVERT: V 46 THR cc_start: 0.8161 (t) cc_final: 0.7622 (m) REVERT: V 88 ILE cc_start: 0.8229 (mp) cc_final: 0.7963 (mt) REVERT: W 114 ILE cc_start: 0.8133 (mm) cc_final: 0.7915 (mm) REVERT: X 51 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.4556 (pm20) REVERT: Y 1 MET cc_start: 0.6516 (tpp) cc_final: 0.6145 (tpp) REVERT: Z 53 LYS cc_start: 0.7356 (mmtt) cc_final: 0.6960 (mmtp) outliers start: 91 outliers final: 71 residues processed: 399 average time/residue: 0.8203 time to fit residues: 551.6331 Evaluate side-chains 397 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 322 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 73 ASP Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 538 random chunks: chunk 483 optimal weight: 6.9990 chunk 367 optimal weight: 6.9990 chunk 254 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 233 optimal weight: 0.7980 chunk 328 optimal weight: 5.9990 chunk 491 optimal weight: 5.9990 chunk 520 optimal weight: 10.0000 chunk 256 optimal weight: 6.9990 chunk 465 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 HIS ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN X 27 ASN Y 12 GLN Z 12 GLN Z 97 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.138 88617 Z= 0.481 Angle : 0.910 11.438 133480 Z= 0.447 Chirality : 0.050 0.391 17202 Planarity : 0.007 0.107 6446 Dihedral : 23.734 179.677 46379 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 5.56 % Allowed : 17.43 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.03 (0.14), residues: 2619 helix: -2.21 (0.18), residues: 629 sheet: -1.29 (0.21), residues: 554 loop : -2.23 (0.14), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 213 HIS 0.007 0.002 HIS B 230 PHE 0.021 0.003 PHE S 129 TYR 0.020 0.003 TYR a 101 ARG 0.011 0.001 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 327 time to evaluate : 3.322 Fit side-chains REVERT: A 8 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6305 (mt-10) REVERT: A 68 SER cc_start: 0.6368 (p) cc_final: 0.5984 (m) REVERT: A 108 LYS cc_start: 0.6524 (mtmm) cc_final: 0.5169 (mtmm) REVERT: C 74 MET cc_start: 0.6222 (ptm) cc_final: 0.5974 (ptm) REVERT: C 114 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6073 (ttpp) REVERT: E 31 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6706 (tp30) REVERT: F 14 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.5719 (tp30) REVERT: F 25 TYR cc_start: 0.7957 (m-80) cc_final: 0.7694 (m-80) REVERT: G 58 GLU cc_start: 0.5176 (OUTLIER) cc_final: 0.4785 (pm20) REVERT: M 6 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7612 (mt) REVERT: M 15 ARG cc_start: 0.8061 (mmt-90) cc_final: 0.7761 (mmt-90) REVERT: O 1 MET cc_start: 0.5803 (OUTLIER) cc_final: 0.5449 (mmt) REVERT: S 184 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7800 (mt) REVERT: S 201 LYS cc_start: 0.7892 (tptm) cc_final: 0.7484 (tptt) REVERT: V 6 MET cc_start: 0.7124 (mmt) cc_final: 0.6737 (mmt) REVERT: V 88 ILE cc_start: 0.8215 (mp) cc_final: 0.7938 (mt) REVERT: X 51 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.4558 (pm20) REVERT: Z 53 LYS cc_start: 0.7350 (mmtt) cc_final: 0.6949 (mmtp) outliers start: 124 outliers final: 99 residues processed: 416 average time/residue: 0.8459 time to fit residues: 596.6575 Evaluate side-chains 425 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 317 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 176 ASN Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 164 GLU Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain S residue 203 GLU Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 73 ASP Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 27 ASN Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 104 ASN Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 122 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 538 random chunks: chunk 433 optimal weight: 6.9990 chunk 295 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 387 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 443 optimal weight: 3.9990 chunk 359 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 265 optimal weight: 8.9990 chunk 466 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 ASN Y 12 GLN Z 97 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 88617 Z= 0.409 Angle : 0.836 11.393 133480 Z= 0.415 Chirality : 0.047 0.378 17202 Planarity : 0.007 0.093 6446 Dihedral : 23.683 179.207 46379 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 6.09 % Allowed : 18.01 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.14), residues: 2619 helix: -2.09 (0.18), residues: 629 sheet: -1.26 (0.21), residues: 560 loop : -2.25 (0.14), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 213 HIS 0.006 0.002 HIS B 230 PHE 0.027 0.003 PHE L 87 TYR 0.020 0.003 TYR a 101 ARG 0.009 0.001 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 330 time to evaluate : 3.320 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6178 (mt-10) REVERT: A 68 SER cc_start: 0.6397 (p) cc_final: 0.5999 (m) REVERT: A 108 LYS cc_start: 0.6485 (mtmm) cc_final: 0.5088 (mtmm) REVERT: E 31 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6711 (tp30) REVERT: F 14 GLU cc_start: 0.6091 (OUTLIER) cc_final: 0.5683 (tp30) REVERT: F 25 TYR cc_start: 0.7937 (m-80) cc_final: 0.7717 (m-80) REVERT: G 58 GLU cc_start: 0.5159 (OUTLIER) cc_final: 0.4784 (pm20) REVERT: L 123 LYS cc_start: 0.6184 (OUTLIER) cc_final: 0.5658 (mmtt) REVERT: M 6 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7608 (mt) REVERT: M 15 ARG cc_start: 0.8038 (mmt-90) cc_final: 0.7711 (mmt-90) REVERT: O 1 MET cc_start: 0.5538 (OUTLIER) cc_final: 0.5165 (mmt) REVERT: S 82 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8481 (pt0) REVERT: S 151 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7800 (mtpt) REVERT: S 184 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7800 (mt) REVERT: S 201 LYS cc_start: 0.7888 (tptm) cc_final: 0.7500 (tptt) REVERT: V 46 THR cc_start: 0.8230 (t) cc_final: 0.7673 (m) REVERT: V 88 ILE cc_start: 0.8202 (mp) cc_final: 0.7926 (mt) REVERT: Z 53 LYS cc_start: 0.7361 (mmtt) cc_final: 0.6955 (mmtp) outliers start: 136 outliers final: 107 residues processed: 432 average time/residue: 0.8015 time to fit residues: 586.5474 Evaluate side-chains 444 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 327 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 210 GLU Chi-restraints excluded: chain L residue 213 THR Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 151 LYS Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 166 SER Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain S residue 203 GLU Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 73 ASP Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 27 ASN Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 104 ASN Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 122 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 538 random chunks: chunk 174 optimal weight: 5.9990 chunk 468 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 305 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 520 optimal weight: 9.9990 chunk 432 optimal weight: 9.9990 chunk 241 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 273 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 ASN Y 12 GLN Z 97 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.150 88617 Z= 0.503 Angle : 0.936 12.517 133480 Z= 0.458 Chirality : 0.051 0.403 17202 Planarity : 0.008 0.104 6446 Dihedral : 23.759 179.796 46379 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 7.39 % Allowed : 18.10 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.14), residues: 2619 helix: -2.22 (0.18), residues: 629 sheet: -1.29 (0.21), residues: 544 loop : -2.33 (0.14), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 213 HIS 0.008 0.002 HIS B 230 PHE 0.024 0.003 PHE L 87 TYR 0.024 0.003 TYR a 101 ARG 0.011 0.001 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 319 time to evaluate : 3.293 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6282 (mt-10) REVERT: A 68 SER cc_start: 0.6511 (p) cc_final: 0.6168 (m) REVERT: A 108 LYS cc_start: 0.6537 (mtmm) cc_final: 0.5093 (mtmm) REVERT: C 114 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6228 (mtpp) REVERT: E 31 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6762 (tp30) REVERT: F 14 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.5683 (tp30) REVERT: F 25 TYR cc_start: 0.7886 (m-80) cc_final: 0.7681 (m-80) REVERT: G 58 GLU cc_start: 0.5149 (OUTLIER) cc_final: 0.4771 (pm20) REVERT: L 156 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7567 (mpp) REVERT: M 6 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7637 (mt) REVERT: M 15 ARG cc_start: 0.8040 (mmt-90) cc_final: 0.7715 (mmt-90) REVERT: O 1 MET cc_start: 0.5536 (OUTLIER) cc_final: 0.5162 (mmt) REVERT: S 82 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8473 (pt0) REVERT: S 184 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7858 (mt) REVERT: S 201 LYS cc_start: 0.7928 (tptm) cc_final: 0.7518 (tptt) REVERT: V 46 THR cc_start: 0.8236 (t) cc_final: 0.7679 (m) REVERT: V 88 ILE cc_start: 0.8201 (mp) cc_final: 0.7923 (mt) REVERT: X 51 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.4533 (pm20) REVERT: Z 53 LYS cc_start: 0.7285 (mmtt) cc_final: 0.6879 (mmtp) outliers start: 165 outliers final: 129 residues processed: 442 average time/residue: 0.8012 time to fit residues: 601.8484 Evaluate side-chains 456 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 316 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain L residue 156 MET Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 176 ASN Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 213 THR Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain Q residue 15 LYS Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 24 MET Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 166 SER Chi-restraints excluded: chain S residue 177 THR Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain S residue 203 GLU Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 73 ASP Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 27 ASN Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 104 ASN Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 122 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 538 random chunks: chunk 501 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 296 optimal weight: 6.9990 chunk 380 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 438 optimal weight: 4.9990 chunk 290 optimal weight: 8.9990 chunk 518 optimal weight: 5.9990 chunk 324 optimal weight: 7.9990 chunk 316 optimal weight: 4.9990 chunk 239 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN X 27 ASN Y 12 GLN Z 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.136 88617 Z= 0.464 Angle : 0.891 12.262 133480 Z= 0.439 Chirality : 0.050 0.393 17202 Planarity : 0.007 0.098 6446 Dihedral : 23.749 179.493 46379 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 7.35 % Allowed : 18.95 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.14), residues: 2619 helix: -2.20 (0.18), residues: 636 sheet: -1.29 (0.21), residues: 549 loop : -2.32 (0.14), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 213 HIS 0.007 0.002 HIS B 230 PHE 0.019 0.003 PHE L 87 TYR 0.025 0.003 TYR a 101 ARG 0.010 0.001 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 318 time to evaluate : 3.360 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6227 (mt-10) REVERT: A 68 SER cc_start: 0.6492 (p) cc_final: 0.6155 (m) REVERT: A 108 LYS cc_start: 0.6551 (mtmm) cc_final: 0.5090 (mtmm) REVERT: C 114 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6124 (ttpp) REVERT: E 31 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6812 (tp30) REVERT: F 14 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5679 (tp30) REVERT: F 25 TYR cc_start: 0.7935 (m-80) cc_final: 0.7553 (m-80) REVERT: G 58 GLU cc_start: 0.5121 (OUTLIER) cc_final: 0.4745 (pm20) REVERT: L 156 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7554 (mpp) REVERT: M 6 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7617 (mt) REVERT: M 46 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7630 (mt0) REVERT: O 1 MET cc_start: 0.5532 (OUTLIER) cc_final: 0.5164 (mmt) REVERT: S 82 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8490 (pt0) REVERT: S 151 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7430 (mtpt) REVERT: S 184 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7852 (mt) REVERT: S 201 LYS cc_start: 0.7930 (tptm) cc_final: 0.7526 (tptt) REVERT: V 46 THR cc_start: 0.8227 (t) cc_final: 0.7694 (m) REVERT: V 88 ILE cc_start: 0.8200 (mp) cc_final: 0.7922 (mt) REVERT: X 51 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.4516 (pm20) REVERT: Z 53 LYS cc_start: 0.7337 (mmtt) cc_final: 0.6905 (mmtp) REVERT: I 25 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5410 (tt0) outliers start: 164 outliers final: 138 residues processed: 439 average time/residue: 0.7920 time to fit residues: 591.9823 Evaluate side-chains 465 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 313 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain L residue 156 MET Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 176 ASN Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 213 THR Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain Q residue 15 LYS Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 24 MET Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 38 ASN Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 151 LYS Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 164 GLU Chi-restraints excluded: chain S residue 166 SER Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain S residue 203 GLU Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 133 HIS Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 73 ASP Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 27 ASN Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 104 ASN Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 88 GLU Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 122 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 538 random chunks: chunk 320 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 309 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 329 optimal weight: 4.9990 chunk 353 optimal weight: 6.9990 chunk 256 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 407 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 ASN Y 12 GLN Z 97 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 88617 Z= 0.275 Angle : 0.678 10.592 133480 Z= 0.345 Chirality : 0.040 0.341 17202 Planarity : 0.006 0.068 6446 Dihedral : 23.447 178.052 46379 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 5.11 % Allowed : 21.59 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.15), residues: 2619 helix: -1.77 (0.19), residues: 629 sheet: -1.18 (0.21), residues: 560 loop : -2.21 (0.14), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 213 HIS 0.006 0.001 HIS C 29 PHE 0.015 0.002 PHE L 87 TYR 0.018 0.002 TYR a 101 ARG 0.008 0.001 ARG I 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 325 time to evaluate : 3.335 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6119 (mt-10) REVERT: A 68 SER cc_start: 0.6630 (p) cc_final: 0.6245 (m) REVERT: A 108 LYS cc_start: 0.6490 (mtmm) cc_final: 0.5040 (mtmm) REVERT: C 114 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6165 (ttpp) REVERT: F 25 TYR cc_start: 0.7857 (m-80) cc_final: 0.7539 (m-80) REVERT: G 58 GLU cc_start: 0.5112 (OUTLIER) cc_final: 0.4709 (pm20) REVERT: L 156 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7412 (mpp) REVERT: M 6 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7542 (mt) REVERT: M 15 ARG cc_start: 0.8004 (mmt-90) cc_final: 0.7689 (mmt-90) REVERT: M 46 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7543 (mt0) REVERT: M 51 LYS cc_start: 0.8444 (ttmt) cc_final: 0.8147 (ptpp) REVERT: S 151 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7431 (mtpt) REVERT: S 184 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7790 (mt) REVERT: S 201 LYS cc_start: 0.7854 (tptm) cc_final: 0.7583 (tptt) REVERT: V 88 ILE cc_start: 0.8167 (mp) cc_final: 0.7897 (mt) REVERT: X 51 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.4394 (pm20) REVERT: Z 53 LYS cc_start: 0.7323 (mmtt) cc_final: 0.6893 (mmtp) outliers start: 114 outliers final: 96 residues processed: 406 average time/residue: 0.8209 time to fit residues: 563.4917 Evaluate side-chains 425 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 320 time to evaluate : 3.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 156 MET Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 24 MET Chi-restraints excluded: chain S residue 38 ASN Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 151 LYS Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 133 HIS Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 73 ASP Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 27 ASN Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 104 ASN Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 88 GLU Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 538 random chunks: chunk 471 optimal weight: 8.9990 chunk 496 optimal weight: 8.9990 chunk 453 optimal weight: 7.9990 chunk 483 optimal weight: 6.9990 chunk 290 optimal weight: 9.9990 chunk 210 optimal weight: 0.1980 chunk 379 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 436 optimal weight: 6.9990 chunk 457 optimal weight: 6.9990 chunk 481 optimal weight: 6.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN Z 97 GLN I 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.143 88617 Z= 0.506 Angle : 0.943 12.069 133480 Z= 0.461 Chirality : 0.052 0.397 17202 Planarity : 0.007 0.102 6446 Dihedral : 23.794 179.969 46379 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 6.09 % Allowed : 20.61 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.06 (0.14), residues: 2619 helix: -2.11 (0.18), residues: 634 sheet: -1.31 (0.21), residues: 544 loop : -2.31 (0.14), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 213 HIS 0.007 0.002 HIS B 230 PHE 0.022 0.003 PHE G 85 TYR 0.024 0.003 TYR a 101 ARG 0.011 0.001 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 322 time to evaluate : 3.347 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6248 (mt-10) REVERT: A 108 LYS cc_start: 0.6498 (mtmm) cc_final: 0.5056 (ttmm) REVERT: C 114 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6090 (mtpp) REVERT: E 31 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6798 (tp30) REVERT: F 25 TYR cc_start: 0.7964 (m-80) cc_final: 0.7605 (m-80) REVERT: G 58 GLU cc_start: 0.5147 (OUTLIER) cc_final: 0.4691 (pm20) REVERT: H 45 GLU cc_start: 0.6174 (OUTLIER) cc_final: 0.5472 (tp30) REVERT: L 156 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7558 (mpp) REVERT: M 6 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7624 (mt) REVERT: M 15 ARG cc_start: 0.8140 (mmt-90) cc_final: 0.7808 (mmt-90) REVERT: M 46 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: S 82 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8507 (pt0) REVERT: S 151 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7422 (mtpt) REVERT: S 184 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7873 (mt) REVERT: S 201 LYS cc_start: 0.7970 (tptm) cc_final: 0.7549 (tptt) REVERT: V 88 ILE cc_start: 0.8197 (mp) cc_final: 0.7916 (mt) REVERT: X 51 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.4462 (pm20) REVERT: Z 53 LYS cc_start: 0.7319 (mmtt) cc_final: 0.6915 (mmtp) REVERT: I 25 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5638 (tt0) outliers start: 136 outliers final: 111 residues processed: 422 average time/residue: 0.8008 time to fit residues: 572.5837 Evaluate side-chains 439 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 315 time to evaluate : 3.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 156 MET Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 176 ASN Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 24 MET Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 151 LYS Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 177 THR Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain S residue 203 GLU Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 133 HIS Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 73 ASP Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 104 ASN Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 88 GLU Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 538 random chunks: chunk 317 optimal weight: 4.9990 chunk 510 optimal weight: 6.9990 chunk 311 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 chunk 355 optimal weight: 9.9990 chunk 535 optimal weight: 0.8980 chunk 493 optimal weight: 3.9990 chunk 426 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 329 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN Z 97 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 88617 Z= 0.336 Angle : 0.769 11.047 133480 Z= 0.389 Chirality : 0.045 0.364 17202 Planarity : 0.006 0.078 6446 Dihedral : 23.689 178.431 46379 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.42 % Allowed : 21.24 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.14), residues: 2619 helix: -1.92 (0.19), residues: 632 sheet: -1.29 (0.21), residues: 558 loop : -2.26 (0.14), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 213 HIS 0.006 0.001 HIS C 29 PHE 0.017 0.002 PHE V 5 TYR 0.021 0.002 TYR a 101 ARG 0.009 0.001 ARG I 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 324 time to evaluate : 3.332 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6050 (mt-10) REVERT: A 68 SER cc_start: 0.6558 (p) cc_final: 0.6147 (m) REVERT: A 108 LYS cc_start: 0.6459 (mtmm) cc_final: 0.4962 (ttmm) REVERT: C 114 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6151 (ttpp) REVERT: F 14 GLU cc_start: 0.6009 (OUTLIER) cc_final: 0.5605 (tp30) REVERT: F 25 TYR cc_start: 0.7914 (m-80) cc_final: 0.7585 (m-80) REVERT: G 58 GLU cc_start: 0.5146 (OUTLIER) cc_final: 0.4693 (pm20) REVERT: H 45 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5437 (tp30) REVERT: M 6 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7577 (mt) REVERT: M 15 ARG cc_start: 0.8028 (mmt-90) cc_final: 0.7751 (mmt-90) REVERT: M 46 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: S 82 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8511 (pt0) REVERT: S 151 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7417 (mtpt) REVERT: S 184 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7792 (mt) REVERT: S 201 LYS cc_start: 0.7920 (tptm) cc_final: 0.7609 (tptt) REVERT: V 46 THR cc_start: 0.8033 (t) cc_final: 0.7563 (m) REVERT: V 88 ILE cc_start: 0.8183 (mp) cc_final: 0.7913 (mt) REVERT: X 51 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.4458 (pm20) REVERT: Z 53 LYS cc_start: 0.7318 (mmtt) cc_final: 0.6910 (mmtp) REVERT: I 25 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.5611 (tt0) outliers start: 121 outliers final: 104 residues processed: 411 average time/residue: 0.8016 time to fit residues: 557.8616 Evaluate side-chains 440 residues out of total 2233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 324 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 213 THR Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 24 MET Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 151 LYS Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 177 THR Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 203 GLU Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 42 LYS Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 133 HIS Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 73 ASP Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 104 ASN Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 88 GLU Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 122 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 538 random chunks: chunk 339 optimal weight: 5.9990 chunk 454 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 393 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 427 optimal weight: 9.9990 chunk 178 optimal weight: 0.7980 chunk 438 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.153349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.133827 restraints weight = 91811.995| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 0.65 r_work: 0.3124 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 88617 Z= 0.253 Angle : 0.696 12.702 133480 Z= 0.356 Chirality : 0.041 0.393 17202 Planarity : 0.005 0.066 6446 Dihedral : 23.591 178.017 46379 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.29 % Allowed : 21.51 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.15), residues: 2619 helix: -1.71 (0.19), residues: 633 sheet: -1.24 (0.21), residues: 564 loop : -2.21 (0.14), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 213 HIS 0.007 0.001 HIS C 29 PHE 0.012 0.002 PHE A 61 TYR 0.023 0.002 TYR a 101 ARG 0.010 0.001 ARG I 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11736.49 seconds wall clock time: 207 minutes 48.05 seconds (12468.05 seconds total)