Starting phenix.real_space_refine on Mon Feb 19 18:11:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttu_26124/02_2024/7ttu_26124.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttu_26124/02_2024/7ttu_26124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttu_26124/02_2024/7ttu_26124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttu_26124/02_2024/7ttu_26124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttu_26124/02_2024/7ttu_26124.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttu_26124/02_2024/7ttu_26124.pdb" } resolution = 3.0 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2784 5.49 5 S 57 5.16 5 C 39764 2.51 5 N 14994 2.21 5 O 23125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "L GLU 29": "OE1" <-> "OE2" Residue "L GLU 90": "OE1" <-> "OE2" Residue "S GLU 138": "OE1" <-> "OE2" Residue "S GLU 159": "OE1" <-> "OE2" Residue "S GLU 196": "OE1" <-> "OE2" Residue "V GLU 32": "OE1" <-> "OE2" Residue "W GLU 18": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 80724 Number of models: 1 Model: "" Number of chains: 27 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: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2085 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 17, 'TRANS': 255} 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} Link IDs: {'PTRANS': 4, 'TRANS': 106} 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: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 698 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 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: "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: "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: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 503 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} 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: {'PTRANS': 1, 'TRANS': 108} Chain breaks: 1 Chain: "1" Number of atoms: 57543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2684, 57543 Inner-chain residues flagged as termini: ['pdbres=" G 1 291 "', 'pdbres=" A 1 318 "', 'pdbres=" C 1 943 "', 'pdbres=" A 11092 "', 'pdbres=" G 11154 "', 'pdbres=" A 11459 "', 'pdbres=" G 11556 "', 'pdbres=" C 11587 "', 'pdbres=" G 12217 "'] Classifications: {'RNA': 2684} Modifications used: {'5*END': 10, 'rna2p_pur': 274, 'rna2p_pyr': 133, 'rna3p_pur': 1274, 'rna3p_pyr': 1003} Link IDs: {'rna2p': 407, 'rna3p': 2276} Chain breaks: 1 Chain: "2" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 2361 Classifications: {'RNA': 111} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 47} Link IDs: {'rna2p': 12, 'rna3p': 98} Time building chain proxies: 33.09, per 1000 atoms: 0.41 Number of scatterers: 80724 At special positions: 0 Unit cell: (208.535, 238.07, 185.265, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 2784 15.00 O 23125 8.00 N 14994 7.00 C 39764 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.82 Conformation dependent library (CDL) restraints added in 3.9 seconds 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4840 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 40 sheets defined 26.2% alpha, 21.0% beta 667 base pairs and 1374 stacking pairs defined. Time for finding SS restraints: 26.54 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 removed outlier: 3.533A pdb=" N VAL A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.544A pdb=" N SER A 104 " --> pdb=" O TYR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.932A pdb=" N ALA A 109 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG A 111 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' 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 203 removed outlier: 3.597A pdb=" N HIS B 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU B 201 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 203 " --> pdb=" O HIS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 213 removed outlier: 3.739A pdb=" N SER B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.519A pdb=" N VAL B 224 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B 225 " --> pdb=" O GLY B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 225' Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.861A pdb=" N ASP B 267 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 268 " --> pdb=" O SER B 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 268' Processing helix chain 'C' and resid 9 through 21 removed outlier: 3.945A pdb=" N LYS C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.598A pdb=" N HIS C 29 " --> pdb=" O GLY C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 70 removed outlier: 3.654A pdb=" N GLN C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG C 55 " --> pdb=" O ARG C 51 " (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 87 removed outlier: 3.819A pdb=" N ASN C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.557A pdb=" N ILE C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 removed outlier: 3.586A pdb=" N ALA C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 108 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 removed outlier: 4.083A pdb=" N LEU E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 38 Processing helix chain 'E' and resid 43 through 61 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 13 through 20 removed outlier: 3.855A pdb=" N GLU F 18 " --> pdb=" O GLU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 46 removed outlier: 3.907A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU F 44 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 25 removed outlier: 3.590A pdb=" N LEU H 18 " --> pdb=" O THR H 14 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS H 19 " --> pdb=" O ARG H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 56 removed outlier: 3.808A pdb=" N LYS H 50 " --> pdb=" O VAL H 46 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL H 51 " --> pdb=" O GLU H 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 55 Processing helix chain 'K' and resid 9 through 21 removed outlier: 3.826A pdb=" N ILE K 14 " --> pdb=" O THR K 10 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU K 15 " --> pdb=" O THR K 11 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE K 18 " --> pdb=" O ILE K 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS K 19 " --> pdb=" O GLU K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 35 removed outlier: 3.510A pdb=" N PHE K 30 " --> pdb=" O PHE K 26 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU K 32 " --> pdb=" O LEU K 28 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 60 removed outlier: 3.547A pdb=" N THR K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 77 removed outlier: 3.579A pdb=" N HIS L 76 " --> pdb=" O PRO L 72 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA L 77 " --> pdb=" O ALA L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'L' and resid 106 through 110 removed outlier: 3.609A pdb=" N THR L 109 " --> pdb=" O SER L 106 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE L 110 " --> pdb=" O VAL L 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 106 through 110' Processing helix chain 'L' and resid 129 through 135 Processing helix chain 'L' and resid 157 through 161 removed outlier: 3.902A pdb=" N SER L 161 " --> pdb=" O SER L 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 26 removed outlier: 3.521A pdb=" N LEU M 26 " --> pdb=" O THR M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 50 removed outlier: 3.574A pdb=" N GLN M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL M 50 " --> pdb=" O GLN M 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 17 Processing helix chain 'P' and resid 9 through 18 removed outlier: 3.516A pdb=" N HIS P 17 " --> pdb=" O HIS P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 23 Processing helix chain 'P' and resid 25 through 39 removed outlier: 3.719A pdb=" N LYS P 30 " --> pdb=" O LYS P 26 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL P 31 " --> pdb=" O ASN P 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 12 removed outlier: 3.524A pdb=" N LYS Q 12 " --> pdb=" O ARG Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 36 removed outlier: 3.650A pdb=" N ASN Q 35 " --> pdb=" O LEU Q 32 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS Q 36 " --> pdb=" O PHE Q 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 32 through 36' Processing helix chain 'Q' and resid 37 through 44 Processing helix chain 'Q' and resid 51 through 56 Processing helix chain 'R' and resid 29 through 33 removed outlier: 3.731A pdb=" N LYS R 33 " --> pdb=" O PRO R 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 44 Processing helix chain 'S' and resid 102 through 120 removed outlier: 3.662A pdb=" N LEU S 108 " --> pdb=" O LYS S 104 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA S 113 " --> pdb=" O ALA S 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU S 120 " --> pdb=" O PHE S 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 147 Processing helix chain 'S' and resid 160 through 166 Processing helix chain 'S' and resid 182 through 189 removed outlier: 3.721A pdb=" N ILE S 186 " --> pdb=" O ASN S 182 " (cutoff:3.500A) Processing helix chain 'S' and resid 196 through 206 Processing helix chain 'V' and resid 25 through 38 removed outlier: 3.645A pdb=" N GLU V 32 " --> pdb=" O ARG V 28 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER V 35 " --> pdb=" O SER V 31 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE V 36 " --> pdb=" O GLU V 32 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG V 38 " --> pdb=" O ALA V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 73 removed outlier: 3.670A pdb=" N LYS V 73 " --> pdb=" O LYS V 69 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 97 removed outlier: 3.709A pdb=" N ARG V 95 " --> pdb=" O GLY V 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 108 removed outlier: 3.544A pdb=" N LEU V 101 " --> pdb=" O ASN V 97 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE V 102 " --> pdb=" O PRO V 98 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER V 105 " --> pdb=" O LEU V 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 120 Processing helix chain 'W' and resid 103 through 107 removed outlier: 3.518A pdb=" N LEU W 106 " --> pdb=" O ALA W 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 112 through 118 Processing helix chain 'X' and resid 56 through 60 Processing helix chain 'X' and resid 80 through 85 removed outlier: 4.170A pdb=" N LYS X 84 " --> pdb=" O GLN X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 92 through 97 removed outlier: 3.572A pdb=" N VAL X 97 " --> pdb=" O PRO X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 129 through 139 removed outlier: 3.848A pdb=" N GLU X 134 " --> pdb=" O ALA X 130 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA X 135 " --> pdb=" O SER X 131 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE X 136 " --> pdb=" O ALA X 132 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS X 139 " --> pdb=" O ALA X 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 56 removed outlier: 3.577A pdb=" N SER Y 49 " --> pdb=" O ARG Y 45 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG Y 56 " --> pdb=" O ILE Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 110 through 123 removed outlier: 3.507A pdb=" N GLU Y 116 " --> pdb=" O GLU Y 112 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS Y 123 " --> pdb=" O ARG Y 119 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 27 removed outlier: 3.608A pdb=" N LYS Z 14 " --> pdb=" O SER Z 10 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA Z 15 " --> pdb=" O ASP Z 11 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE Z 25 " --> pdb=" O ALA Z 21 " (cutoff:3.500A) Processing helix chain 'Z' and resid 34 through 54 removed outlier: 3.854A pdb=" N GLU Z 39 " --> pdb=" O ALA Z 35 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG Z 41 " --> pdb=" O ALA Z 37 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N SER Z 42 " --> pdb=" O LYS Z 38 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL Z 43 " --> pdb=" O GLU Z 39 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR Z 49 " --> pdb=" O GLU Z 45 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU Z 50 " --> pdb=" O LYS Z 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS Z 53 " --> pdb=" O THR Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 61 Processing helix chain 'Z' and resid 81 through 88 Processing helix chain 'a' and resid 8 through 17 removed outlier: 3.511A pdb=" N ARG a 17 " --> pdb=" O LYS a 13 " (cutoff:3.500A) Processing helix chain 'a' and resid 69 through 87 removed outlier: 3.688A pdb=" N LYS a 75 " --> pdb=" O GLU a 71 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU a 78 " --> pdb=" O THR a 74 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP a 86 " --> pdb=" O LYS a 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS a 87 " --> pdb=" O LYS a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 114 removed outlier: 3.877A pdb=" N ALA a 109 " --> pdb=" O VAL a 105 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU a 110 " --> pdb=" O LYS a 106 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA a 111 " --> pdb=" O ALA a 107 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA a 112 " --> pdb=" O LEU a 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 88 removed outlier: 6.846A pdb=" N ILE A 83 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ARG A 33 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS A 85 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N GLU A 46 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 66 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A 62 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARG A 52 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.760A 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 34 through 35 Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 105 removed outlier: 6.634A pdb=" N ILE B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE B 81 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 93 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 129 through 131 removed outlier: 5.773A pdb=" N VAL B 164 " --> pdb=" O ARG B 175 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG B 175 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 166 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET B 183 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 5.973A 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: 6.560A 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: 4.059A pdb=" N PHE D 40 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLU D 6 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL D 38 " --> pdb=" O GLU D 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.824A pdb=" N GLN D 18 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS D 94 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP D 98 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR D 59 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 77 removed outlier: 4.207A 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: 5.991A pdb=" N SER E 101 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU E 73 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER E 108 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL E 71 " --> pdb=" O SER E 108 " (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: 6.525A pdb=" N ASP F 28 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR F 26 " --> pdb=" O PRO F 10 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ARG F 76 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER F 52 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 62 through 65 removed outlier: 3.595A pdb=" N GLY F 70 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET F 65 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR F 68 " --> pdb=" O MET F 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 63 through 64 removed outlier: 3.784A pdb=" N ALA G 25 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN G 8 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 4.012A 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 Processing sheet with id=AB7, first strand: chain 'G' and resid 81 through 83 Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 5 removed outlier: 6.954A pdb=" N LEU H 4 " --> pdb=" O GLY H 64 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASP H 90 " --> pdb=" O ALA H 75 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR H 77 " --> pdb=" O HIS H 88 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS H 88 " --> pdb=" O TYR H 77 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N PHE H 79 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE H 86 " --> pdb=" O PHE H 79 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N LYS H 26 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N ILE H 89 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE H 91 " --> pdb=" O PRO H 28 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL H 30 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA H 93 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR H 32 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL H 39 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLY H 33 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LYS H 37 " --> pdb=" O GLY H 33 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 44 through 47 removed outlier: 6.548A pdb=" N LEU I 67 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE I 68 " --> pdb=" O GLY I 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 54 through 55 Processing sheet with id=AC2, first strand: chain 'J' and resid 13 through 18 Processing sheet with id=AC3, first strand: chain 'J' and resid 33 through 37 Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 16 removed outlier: 5.564A pdb=" N LYS L 9 " --> pdb=" O GLU L 29 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU L 29 " --> pdb=" O LYS L 9 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY L 11 " --> pdb=" O VAL L 27 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL L 194 " --> pdb=" O VAL L 188 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL L 188 " --> pdb=" O VAL L 194 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU L 196 " --> pdb=" O VAL L 186 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU L 184 " --> pdb=" O LYS L 198 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N THR L 179 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLY L 120 " --> pdb=" O THR L 179 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLN L 181 " --> pdb=" O VAL L 118 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL L 118 " --> pdb=" O GLN L 181 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL L 121 " --> pdb=" O LEU L 208 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU L 208 " --> pdb=" O VAL L 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 34 through 39 removed outlier: 6.358A pdb=" N GLN L 50 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS L 38 " --> pdb=" O ALA L 48 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA L 48 " --> pdb=" O LYS L 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 126 through 128 removed outlier: 3.602A pdb=" N GLY L 126 " --> pdb=" O MET L 173 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 34 through 37 Processing sheet with id=AC8, first strand: chain 'N' and resid 27 through 29 Processing sheet with id=AC9, first strand: chain 'O' and resid 17 through 22 Processing sheet with id=AD1, first strand: chain 'Q' and resid 15 through 16 Processing sheet with id=AD2, first strand: chain 'R' and resid 15 through 19 Processing sheet with id=AD3, first strand: chain 'S' and resid 123 through 126 removed outlier: 6.340A pdb=" N LEU S 153 " --> pdb=" O VAL S 193 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N THR S 195 " --> pdb=" O LEU S 153 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL S 155 " --> pdb=" O THR S 195 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL S 152 " --> pdb=" O GLN S 174 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N THR S 176 " --> pdb=" O VAL S 152 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL S 154 " --> pdb=" O THR S 176 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'V' and resid 123 through 125 Processing sheet with id=AD5, first strand: chain 'V' and resid 74 through 78 Processing sheet with id=AD6, first strand: chain 'W' and resid 7 through 10 removed outlier: 6.479A pdb=" N ARG W 17 " --> pdb=" O VAL W 10 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA W 16 " --> pdb=" O ALA W 46 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA W 46 " --> pdb=" O ALA W 16 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU W 18 " --> pdb=" O LYS W 44 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL W 40 " --> pdb=" O ILE W 22 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL W 24 " --> pdb=" O VAL W 38 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N VAL W 38 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA W 83 " --> pdb=" O VAL W 63 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N CYS W 84 " --> pdb=" O ARG W 7 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS W 9 " --> pdb=" O CYS W 84 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE W 86 " --> pdb=" O LYS W 9 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 75 through 78 removed outlier: 6.328A pdb=" N ILE X 109 " --> pdb=" O LYS X 127 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 90 through 91 removed outlier: 7.145A pdb=" N VAL X 123 " --> pdb=" O GLU X 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 63 through 66 removed outlier: 6.522A pdb=" N ILE Y 102 " --> pdb=" O ALA Y 36 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA Y 36 " --> pdb=" O ILE Y 102 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE Y 104 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 40 through 43 removed outlier: 6.029A pdb=" N VAL Y 90 " --> pdb=" O LYS Y 76 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LYS Y 76 " --> pdb=" O VAL Y 90 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY Y 92 " --> pdb=" O TYR Y 74 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Z' and resid 29 through 33 removed outlier: 6.621A pdb=" N SER Z 116 " --> pdb=" O GLN Z 106 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Z' and resid 70 through 71 Processing sheet with id=AE4, first strand: chain 'a' and resid 51 through 57 removed outlier: 6.949A pdb=" N ILE a 44 " --> pdb=" O LEU a 53 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN a 55 " --> pdb=" O ALA a 42 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA a 42 " --> pdb=" O GLN a 55 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER a 57 " --> pdb=" O ILE a 40 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE a 40 " --> pdb=" O SER a 57 " (cutoff:3.500A) 631 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1664 hydrogen bonds 2658 hydrogen bond angles 0 basepair planarities 667 basepair parallelities 1374 stacking parallelities Total time for adding SS restraints: 104.44 Time building geometry restraints manager: 33.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11948 1.33 - 1.45: 38368 1.45 - 1.57: 32186 1.57 - 1.70: 5567 1.70 - 1.82: 100 Bond restraints: 88169 Sorted by residual: bond pdb=" N ILE S 78 " pdb=" CA ILE S 78 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.29e-02 6.01e+03 6.72e+00 bond pdb=" N ARG S 79 " pdb=" CA ARG S 79 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.19e-02 7.06e+03 6.68e+00 bond pdb=" N SER S 58 " pdb=" CA SER S 58 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 6.68e+00 bond pdb=" N ARG P 40 " pdb=" CA ARG P 40 " ideal model delta sigma weight residual 1.456 1.486 -0.031 1.22e-02 6.72e+03 6.35e+00 bond pdb=" N THR S 77 " pdb=" CA THR S 77 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.32e-02 5.74e+03 5.60e+00 ... (remaining 88164 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.09: 15681 106.09 - 113.16: 51794 113.16 - 120.22: 32649 120.22 - 127.29: 26546 127.29 - 134.35: 6137 Bond angle restraints: 132807 Sorted by residual: angle pdb=" N ILE W 2 " pdb=" CA ILE W 2 " pdb=" C ILE W 2 " ideal model delta sigma weight residual 111.62 108.54 3.08 7.90e-01 1.60e+00 1.52e+01 angle pdb=" O3' A 11997 " pdb=" C3' A 11997 " pdb=" C2' A 11997 " ideal model delta sigma weight residual 109.50 114.78 -5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" CA THR S 77 " pdb=" C THR S 77 " pdb=" O THR S 77 " ideal model delta sigma weight residual 121.51 117.83 3.68 1.12e+00 7.97e-01 1.08e+01 angle pdb=" N ILE S 78 " pdb=" CA ILE S 78 " pdb=" C ILE S 78 " ideal model delta sigma weight residual 112.80 109.06 3.74 1.15e+00 7.56e-01 1.06e+01 angle pdb=" C ALA D 50 " pdb=" N PRO D 51 " pdb=" CA PRO D 51 " ideal model delta sigma weight residual 127.00 134.35 -7.35 2.40e+00 1.74e-01 9.39e+00 ... (remaining 132802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 49913 35.76 - 71.52: 5717 71.52 - 107.27: 663 107.27 - 143.03: 12 143.03 - 178.79: 30 Dihedral angle restraints: 56335 sinusoidal: 48803 harmonic: 7532 Sorted by residual: dihedral pdb=" O4' U 1 403 " pdb=" C1' U 1 403 " pdb=" N1 U 1 403 " pdb=" C2 U 1 403 " ideal model delta sinusoidal sigma weight residual -160.00 18.79 -178.79 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 -160.00 11.51 -171.51 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U 12655 " pdb=" C1' U 12655 " pdb=" N1 U 12655 " pdb=" C2 U 12655 " ideal model delta sinusoidal sigma weight residual 200.00 32.68 167.32 1 1.50e+01 4.44e-03 8.43e+01 ... (remaining 56332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 15623 0.050 - 0.101: 1183 0.101 - 0.151: 277 0.151 - 0.202: 28 0.202 - 0.252: 5 Chirality restraints: 17116 Sorted by residual: chirality pdb=" C1' U 12607 " pdb=" O4' U 12607 " pdb=" C2' U 12607 " pdb=" N1 U 12607 " both_signs ideal model delta sigma weight residual False 2.47 2.21 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C2' C 11932 " pdb=" C3' C 11932 " pdb=" O2' C 11932 " pdb=" C1' C 11932 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C1' A 11027 " pdb=" O4' A 11027 " pdb=" C2' A 11027 " pdb=" N9 A 11027 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 17113 not shown) Planarity restraints: 6410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 12892 " -0.034 2.00e-02 2.50e+03 1.55e-02 7.18e+00 pdb=" N9 G 12892 " 0.040 2.00e-02 2.50e+03 pdb=" C8 G 12892 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G 12892 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G 12892 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G 12892 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G 12892 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G 12892 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G 12892 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G 12892 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G 12892 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G 12892 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11954 " -0.032 2.00e-02 2.50e+03 1.45e-02 5.77e+00 pdb=" N9 A 11954 " 0.034 2.00e-02 2.50e+03 pdb=" C8 A 11954 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 11954 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 11954 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A 11954 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A 11954 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A 11954 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 11954 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 11954 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A 11954 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11979 " 0.032 2.00e-02 2.50e+03 1.42e-02 5.57e+00 pdb=" N9 A 11979 " -0.032 2.00e-02 2.50e+03 pdb=" C8 A 11979 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A 11979 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A 11979 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A 11979 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A 11979 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A 11979 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A 11979 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A 11979 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A 11979 " -0.005 2.00e-02 2.50e+03 ... (remaining 6407 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 7141 2.72 - 3.26: 66245 3.26 - 3.81: 148963 3.81 - 4.35: 204942 4.35 - 4.90: 272060 Nonbonded interactions: 699351 Sorted by model distance: nonbonded pdb=" NZ LYS I 85 " pdb=" OP1 A 1 902 " model vdw 2.175 2.520 nonbonded pdb=" OE2 GLU L 90 " pdb=" O2' U 12662 " model vdw 2.179 2.440 nonbonded pdb=" OP2 U 12885 " pdb=" O2' G 12886 " model vdw 2.180 2.440 nonbonded pdb=" O2' G 11725 " pdb=" O2' A 11789 " model vdw 2.180 2.440 nonbonded pdb=" O LYS G 42 " pdb=" O2' A 1 526 " model vdw 2.189 2.440 ... (remaining 699346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 4.160 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: 0.050 Extract box with map and model: 20.460 Check model and map are aligned: 0.900 Set scattering table: 0.550 Process input model: 255.370 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 294.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 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 0.038 88169 Z= 0.115 Angle : 0.456 8.108 132807 Z= 0.243 Chirality : 0.030 0.252 17116 Planarity : 0.004 0.056 6410 Dihedral : 22.583 178.792 51489 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -1.25 (0.15), residues: 2607 helix: -1.26 (0.20), residues: 612 sheet: 0.25 (0.22), residues: 561 loop : -1.05 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 213 HIS 0.004 0.001 HIS C 29 PHE 0.009 0.001 PHE A 76 TYR 0.018 0.001 TYR H 34 ARG 0.007 0.000 ARG O 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 556 time to evaluate : 3.213 Fit side-chains REVERT: F 50 VAL cc_start: 0.7651 (m) cc_final: 0.7372 (t) REVERT: G 41 MET cc_start: 0.6160 (ppp) cc_final: 0.5940 (mtt) REVERT: S 142 VAL cc_start: 0.6772 (m) cc_final: 0.6549 (t) outliers start: 0 outliers final: 0 residues processed: 556 average time/residue: 1.7405 time to fit residues: 1265.5600 Evaluate side-chains 322 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 452 optimal weight: 7.9990 chunk 406 optimal weight: 9.9990 chunk 225 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 274 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 420 optimal weight: 9.9990 chunk 162 optimal weight: 0.0170 chunk 255 optimal weight: 10.0000 chunk 312 optimal weight: 8.9990 chunk 486 optimal weight: 8.9990 overall best weight: 5.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN C 81 ASN F 57 ASN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 ASN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN L 167 GLN Q 43 GLN S 162 ASN ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 48 HIS X 78 ASN X 114 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.6505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 88169 Z= 0.491 Angle : 0.920 15.578 132807 Z= 0.453 Chirality : 0.050 0.333 17116 Planarity : 0.007 0.080 6410 Dihedral : 23.140 179.771 46114 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.27 % Allowed : 15.06 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -1.82 (0.14), residues: 2607 helix: -1.39 (0.19), residues: 632 sheet: -0.06 (0.22), residues: 516 loop : -1.56 (0.14), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 213 HIS 0.013 0.002 HIS Y 71 PHE 0.027 0.003 PHE A 76 TYR 0.019 0.003 TYR V 126 ARG 0.021 0.001 ARG R 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 408 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.8905 (mt) cc_final: 0.8670 (mt) REVERT: A 90 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6127 (ppp80) REVERT: B 87 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.6703 (mtm-85) REVERT: B 170 LYS cc_start: 0.6729 (pttt) cc_final: 0.6464 (pttm) REVERT: B 255 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8062 (mp) REVERT: C 19 LYS cc_start: 0.8327 (tttt) cc_final: 0.8042 (tppt) REVERT: C 59 LYS cc_start: 0.7886 (mttp) cc_final: 0.7597 (tttt) REVERT: E 72 LYS cc_start: 0.7375 (ttpt) cc_final: 0.7152 (ttmt) REVERT: F 9 ARG cc_start: 0.7189 (mtm180) cc_final: 0.6840 (ttt180) REVERT: F 20 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7857 (mmt) REVERT: G 32 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.5172 (mpt90) REVERT: G 41 MET cc_start: 0.6481 (ppp) cc_final: 0.6206 (mmm) REVERT: G 100 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.5897 (tt0) REVERT: K 21 SER cc_start: 0.7350 (OUTLIER) cc_final: 0.7030 (p) REVERT: K 29 ARG cc_start: 0.7613 (mtt-85) cc_final: 0.6989 (mtm110) REVERT: L 78 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6966 (tmtm) REVERT: S 142 VAL cc_start: 0.7766 (m) cc_final: 0.7519 (t) REVERT: V 10 SER cc_start: 0.8628 (p) cc_final: 0.8229 (m) REVERT: V 121 LYS cc_start: 0.8130 (ptmt) cc_final: 0.7874 (ptpp) REVERT: W 53 LYS cc_start: 0.7611 (mmpt) cc_final: 0.7282 (mtpt) REVERT: W 67 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8252 (p) REVERT: X 106 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8124 (mptt) REVERT: X 134 GLU cc_start: 0.6521 (mp0) cc_final: 0.5849 (pm20) REVERT: Y 52 ILE cc_start: 0.8662 (mm) cc_final: 0.8430 (mt) REVERT: Z 120 GLU cc_start: 0.7964 (pt0) cc_final: 0.7723 (pt0) REVERT: a 35 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7321 (ttm170) REVERT: a 90 LYS cc_start: 0.4978 (pmtt) cc_final: 0.4743 (tptm) outliers start: 95 outliers final: 27 residues processed: 471 average time/residue: 1.7903 time to fit residues: 1100.9016 Evaluate side-chains 363 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 325 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 32 ARG Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 78 LYS Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain Q residue 59 LYS Chi-restraints excluded: chain R residue 2 LYS Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 116 SER Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 35 ARG Chi-restraints excluded: chain a residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 270 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 405 optimal weight: 10.0000 chunk 331 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 487 optimal weight: 5.9990 chunk 526 optimal weight: 10.0000 chunk 434 optimal weight: 8.9990 chunk 483 optimal weight: 8.9990 chunk 166 optimal weight: 0.8980 chunk 391 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN E 60 HIS E 90 GLN I 86 GLN L 50 GLN Q 43 GLN S 162 ASN ** W 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.7173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 88169 Z= 0.314 Angle : 0.693 9.550 132807 Z= 0.353 Chirality : 0.042 0.320 17116 Planarity : 0.006 0.063 6410 Dihedral : 22.974 179.815 46114 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.17 % Allowed : 19.33 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -1.74 (0.14), residues: 2607 helix: -0.96 (0.20), residues: 640 sheet: -0.02 (0.22), residues: 499 loop : -1.68 (0.13), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 213 HIS 0.010 0.002 HIS E 60 PHE 0.019 0.002 PHE C 25 TYR 0.016 0.002 TYR Y 74 ARG 0.007 0.001 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 345 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6013 (ppp80) REVERT: B 35 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7722 (mtpm) REVERT: B 82 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8463 (mt0) REVERT: B 87 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.6719 (mtm-85) REVERT: B 170 LYS cc_start: 0.6709 (pttt) cc_final: 0.6469 (pttp) REVERT: B 236 GLU cc_start: 0.7222 (mm-30) cc_final: 0.7014 (mm-30) REVERT: B 255 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7990 (mp) REVERT: C 19 LYS cc_start: 0.8257 (tttt) cc_final: 0.7893 (tppt) REVERT: C 59 LYS cc_start: 0.7955 (mttp) cc_final: 0.7634 (tttt) REVERT: C 80 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8196 (mmt) REVERT: D 1 MET cc_start: 0.5955 (pmt) cc_final: 0.5227 (ptp) REVERT: D 12 ILE cc_start: 0.8537 (pt) cc_final: 0.8323 (tt) REVERT: F 20 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7756 (mmt) REVERT: G 19 LYS cc_start: 0.7489 (mmmt) cc_final: 0.7262 (tttp) REVERT: G 32 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.5379 (mpt180) REVERT: G 41 MET cc_start: 0.6364 (ppp) cc_final: 0.6077 (mmm) REVERT: G 100 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5873 (tt0) REVERT: K 29 ARG cc_start: 0.7557 (mtt-85) cc_final: 0.6959 (mtm110) REVERT: M 43 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8632 (mm) REVERT: N 17 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.6730 (mtp180) REVERT: P 30 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7565 (tttt) REVERT: R 2 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7964 (mtpt) REVERT: W 17 ARG cc_start: 0.7375 (ttm170) cc_final: 0.6999 (mtp180) REVERT: W 53 LYS cc_start: 0.7706 (mtpt) cc_final: 0.7384 (mtpt) REVERT: X 15 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6510 (mt-10) REVERT: Y 5 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7480 (mtpt) REVERT: Z 10 SER cc_start: 0.8730 (t) cc_final: 0.8475 (p) REVERT: Z 46 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.7893 (mttt) REVERT: Z 53 LYS cc_start: 0.7380 (mttm) cc_final: 0.7174 (mptt) REVERT: Z 89 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8232 (mp) REVERT: a 4 LYS cc_start: 0.5853 (OUTLIER) cc_final: 0.5265 (ptmt) outliers start: 115 outliers final: 44 residues processed: 411 average time/residue: 1.7008 time to fit residues: 926.0096 Evaluate side-chains 379 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 317 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 32 ARG Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 30 LYS Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain R residue 2 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 66 LYS Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain X residue 15 GLU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 46 LYS Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 116 SER Chi-restraints excluded: chain a residue 4 LYS Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 481 optimal weight: 6.9990 chunk 366 optimal weight: 10.0000 chunk 253 optimal weight: 0.4980 chunk 53 optimal weight: 7.9990 chunk 232 optimal weight: 1.9990 chunk 327 optimal weight: 7.9990 chunk 489 optimal weight: 10.0000 chunk 518 optimal weight: 7.9990 chunk 255 optimal weight: 8.9990 chunk 463 optimal weight: 7.9990 chunk 139 optimal weight: 0.5980 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN E 60 HIS L 187 GLN S 174 GLN V 41 ASN W 82 ASN Y 71 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.7567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 88169 Z= 0.308 Angle : 0.701 9.218 132807 Z= 0.357 Chirality : 0.042 0.319 17116 Planarity : 0.006 0.054 6410 Dihedral : 23.001 177.611 46114 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 6.43 % Allowed : 20.91 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -1.71 (0.15), residues: 2607 helix: -0.80 (0.20), residues: 642 sheet: -0.04 (0.22), residues: 507 loop : -1.73 (0.13), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 213 HIS 0.008 0.001 HIS Y 71 PHE 0.019 0.002 PHE C 25 TYR 0.015 0.002 TYR V 126 ARG 0.017 0.001 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 315 time to evaluate : 3.350 Fit side-chains revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6335 (ppp80) REVERT: B 82 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8502 (mt0) REVERT: B 87 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.6703 (mtm-85) REVERT: B 170 LYS cc_start: 0.6609 (pttt) cc_final: 0.6392 (pttp) REVERT: B 236 GLU cc_start: 0.7227 (mm-30) cc_final: 0.7008 (mm-30) REVERT: B 255 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8006 (mp) REVERT: C 19 LYS cc_start: 0.8280 (tttt) cc_final: 0.7910 (tppt) REVERT: C 59 LYS cc_start: 0.7966 (mttp) cc_final: 0.7639 (tttt) REVERT: C 80 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8223 (mmm) REVERT: C 108 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6753 (mt0) REVERT: D 12 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8260 (tt) REVERT: G 41 MET cc_start: 0.6430 (ppp) cc_final: 0.6045 (mmm) REVERT: G 100 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5915 (tt0) REVERT: H 12 LYS cc_start: 0.4995 (OUTLIER) cc_final: 0.4795 (mmtp) REVERT: K 21 SER cc_start: 0.7395 (OUTLIER) cc_final: 0.7127 (p) REVERT: K 29 ARG cc_start: 0.7604 (mtt-85) cc_final: 0.6958 (mtm110) REVERT: N 17 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.6758 (mtp180) REVERT: O 31 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: P 30 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7575 (tttt) REVERT: R 2 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8135 (mtpt) REVERT: R 4 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7931 (mpp80) REVERT: W 53 LYS cc_start: 0.7775 (mtpt) cc_final: 0.7477 (mtpt) REVERT: X 15 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6489 (mt-10) REVERT: Y 5 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7367 (mtpt) REVERT: Y 6 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7151 (ttm170) REVERT: Z 10 SER cc_start: 0.8719 (t) cc_final: 0.8514 (p) REVERT: Z 53 LYS cc_start: 0.7441 (mttm) cc_final: 0.7109 (mptm) REVERT: Z 89 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8229 (mp) outliers start: 143 outliers final: 69 residues processed: 401 average time/residue: 1.6708 time to fit residues: 891.7158 Evaluate side-chains 392 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 304 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 31 GLU Chi-restraints excluded: chain P residue 30 LYS Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain R residue 2 LYS Chi-restraints excluded: chain R residue 4 ARG Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain X residue 10 GLU Chi-restraints excluded: chain X residue 15 GLU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Y residue 52 ILE Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 116 SER Chi-restraints excluded: chain a residue 4 LYS Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 431 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 7 optimal weight: 0.0170 chunk 385 optimal weight: 8.9990 chunk 213 optimal weight: 7.9990 chunk 442 optimal weight: 7.9990 chunk 358 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 465 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 overall best weight: 6.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 60 HIS L 187 GLN Q 43 GLN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 41 ASN W 82 ASN X 4 HIS Z 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.7825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.126 88169 Z= 0.534 Angle : 0.945 10.758 132807 Z= 0.466 Chirality : 0.053 0.380 17116 Planarity : 0.007 0.072 6410 Dihedral : 23.376 177.407 46114 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 7.73 % Allowed : 21.36 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.12 (0.14), residues: 2607 helix: -1.11 (0.19), residues: 638 sheet: -0.45 (0.21), residues: 533 loop : -1.95 (0.13), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 213 HIS 0.010 0.002 HIS E 60 PHE 0.027 0.003 PHE C 25 TYR 0.023 0.003 TYR V 126 ARG 0.009 0.001 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 302 time to evaluate : 3.220 Fit side-chains revert: symmetry clash REVERT: A 87 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6700 (mt-10) REVERT: A 90 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6479 (ppp80) REVERT: B 65 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8325 (mm) REVERT: B 82 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: B 84 ASP cc_start: 0.8414 (t0) cc_final: 0.8064 (t0) REVERT: B 87 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.6623 (mtm-85) REVERT: B 236 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7080 (mm-30) REVERT: B 255 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8177 (mp) REVERT: C 19 LYS cc_start: 0.8361 (tttt) cc_final: 0.8048 (tppt) REVERT: C 80 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8221 (mmm) REVERT: C 115 ASP cc_start: 0.7072 (m-30) cc_final: 0.6808 (t0) REVERT: D 12 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8226 (tt) REVERT: E 60 HIS cc_start: 0.7538 (OUTLIER) cc_final: 0.6644 (t-170) REVERT: F 14 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6495 (mt-10) REVERT: G 41 MET cc_start: 0.6450 (ppp) cc_final: 0.5961 (mmm) REVERT: G 100 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.5923 (tt0) REVERT: H 12 LYS cc_start: 0.4987 (OUTLIER) cc_final: 0.4740 (mmtp) REVERT: K 21 SER cc_start: 0.7576 (OUTLIER) cc_final: 0.7145 (p) REVERT: K 29 ARG cc_start: 0.7621 (mtt-85) cc_final: 0.6952 (mtm110) REVERT: L 100 GLU cc_start: 0.6613 (mm-30) cc_final: 0.6387 (mm-30) REVERT: N 17 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.6827 (mtp180) REVERT: P 30 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7587 (tttt) REVERT: V 102 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8530 (mm) REVERT: W 53 LYS cc_start: 0.7816 (mtpt) cc_final: 0.7492 (mtpt) REVERT: W 66 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8231 (mtpp) REVERT: X 15 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6568 (mt-10) REVERT: Y 5 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7570 (mtpt) REVERT: Y 6 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7066 (ttm170) REVERT: Z 10 SER cc_start: 0.8853 (t) cc_final: 0.8574 (p) REVERT: Z 53 LYS cc_start: 0.7521 (mttm) cc_final: 0.7176 (mptm) REVERT: Z 89 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8312 (mp) REVERT: Z 112 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7835 (t0) outliers start: 172 outliers final: 99 residues processed: 414 average time/residue: 1.6635 time to fit residues: 921.7098 Evaluate side-chains 417 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 296 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 30 LYS Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain R residue 2 LYS Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 66 LYS Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 15 GLU Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 52 ILE Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain Z residue 112 ASP Chi-restraints excluded: chain Z residue 116 SER Chi-restraints excluded: chain a residue 4 LYS Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 78 GLU Chi-restraints excluded: chain a residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 174 optimal weight: 0.9990 chunk 466 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 304 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 518 optimal weight: 4.9990 chunk 430 optimal weight: 8.9990 chunk 240 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 272 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 60 HIS E 61 ASN G 8 ASN I 20 ASN L 187 GLN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN V 41 ASN W 82 ASN X 78 ASN ** a 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.7676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 88169 Z= 0.125 Angle : 0.526 8.894 132807 Z= 0.276 Chirality : 0.034 0.269 17116 Planarity : 0.004 0.057 6410 Dihedral : 22.859 179.391 46114 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.91 % Allowed : 25.45 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -1.48 (0.15), residues: 2607 helix: -0.36 (0.21), residues: 639 sheet: -0.07 (0.22), residues: 541 loop : -1.68 (0.14), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 213 HIS 0.028 0.001 HIS E 60 PHE 0.014 0.001 PHE A 76 TYR 0.017 0.001 TYR E 62 ARG 0.006 0.000 ARG a 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 335 time to evaluate : 3.206 Fit side-chains REVERT: A 90 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.5922 (ppp80) REVERT: A 106 ARG cc_start: 0.6836 (mmp-170) cc_final: 0.6623 (mmm-85) REVERT: C 19 LYS cc_start: 0.8260 (tttt) cc_final: 0.7918 (tppt) REVERT: D 37 LYS cc_start: 0.6674 (mtpm) cc_final: 0.6051 (tttt) REVERT: F 14 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6493 (mt-10) REVERT: G 41 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.5946 (mmm) REVERT: K 21 SER cc_start: 0.7286 (OUTLIER) cc_final: 0.7031 (p) REVERT: K 29 ARG cc_start: 0.7557 (mtt-85) cc_final: 0.6948 (mtm110) REVERT: N 17 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.6790 (mtp180) REVERT: O 1 MET cc_start: 0.5461 (ttp) cc_final: 0.5183 (ptp) REVERT: Z 89 ILE cc_start: 0.8456 (mm) cc_final: 0.8182 (mp) REVERT: a 4 LYS cc_start: 0.5617 (OUTLIER) cc_final: 0.5164 (ptmt) outliers start: 87 outliers final: 35 residues processed: 386 average time/residue: 1.6310 time to fit residues: 841.9008 Evaluate side-chains 355 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 314 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 52 ILE Chi-restraints excluded: chain a residue 4 LYS Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 499 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 295 optimal weight: 20.0000 chunk 378 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 chunk 436 optimal weight: 20.0000 chunk 289 optimal weight: 10.0000 chunk 516 optimal weight: 9.9990 chunk 323 optimal weight: 8.9990 chunk 314 optimal weight: 9.9990 chunk 238 optimal weight: 0.8980 overall best weight: 7.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN C 81 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN L 187 GLN Q 43 GLN V 41 ASN W 82 ASN ** a 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.7917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.144 88169 Z= 0.634 Angle : 1.030 10.933 132807 Z= 0.501 Chirality : 0.056 0.395 17116 Planarity : 0.008 0.078 6410 Dihedral : 23.376 177.958 46114 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 6.97 % Allowed : 24.15 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.15 (0.14), residues: 2607 helix: -1.04 (0.20), residues: 635 sheet: -0.51 (0.21), residues: 537 loop : -2.02 (0.13), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 250 HIS 0.011 0.002 HIS N 19 PHE 0.030 0.003 PHE C 25 TYR 0.027 0.003 TYR V 126 ARG 0.013 0.001 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 305 time to evaluate : 3.492 Fit side-chains REVERT: A 87 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6763 (mt-10) REVERT: A 89 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7495 (tttp) REVERT: A 90 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6533 (ppp80) REVERT: B 13 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8758 (mmt180) REVERT: B 65 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8255 (mm) REVERT: B 87 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7403 (mtt-85) REVERT: C 19 LYS cc_start: 0.8384 (tttt) cc_final: 0.8144 (tppt) REVERT: C 49 ASP cc_start: 0.8485 (m-30) cc_final: 0.8056 (m-30) REVERT: E 60 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.6739 (t-170) REVERT: F 14 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6468 (mt-10) REVERT: G 41 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.5925 (mmm) REVERT: H 12 LYS cc_start: 0.5270 (OUTLIER) cc_final: 0.4921 (tttm) REVERT: K 21 SER cc_start: 0.7705 (OUTLIER) cc_final: 0.7264 (p) REVERT: K 29 ARG cc_start: 0.7636 (mtt-85) cc_final: 0.6966 (mtm110) REVERT: L 44 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: L 100 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6415 (mm-30) REVERT: N 17 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.6835 (mtp180) REVERT: P 30 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7626 (tttt) REVERT: V 64 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6455 (mt-10) REVERT: V 102 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8502 (mm) REVERT: W 53 LYS cc_start: 0.7816 (mtpt) cc_final: 0.7495 (mtpt) REVERT: W 66 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8220 (mtpp) REVERT: X 15 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6565 (mt-10) REVERT: Y 79 LEU cc_start: 0.7557 (mt) cc_final: 0.7296 (mp) REVERT: Z 89 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8326 (mp) REVERT: a 72 LEU cc_start: 0.5626 (OUTLIER) cc_final: 0.5390 (tt) outliers start: 155 outliers final: 93 residues processed: 407 average time/residue: 1.6186 time to fit residues: 886.4631 Evaluate side-chains 412 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 299 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 30 LYS Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain Q residue 31 HIS Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 125 VAL Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 66 LYS Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 15 GLU Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 52 ILE Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 89 ILE Chi-restraints excluded: chain a residue 4 LYS Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 319 optimal weight: 5.9990 chunk 206 optimal weight: 0.9980 chunk 308 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 328 optimal weight: 3.9990 chunk 351 optimal weight: 5.9990 chunk 255 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 406 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN B 133 GLN E 60 HIS E 61 ASN L 187 GLN S 174 GLN V 41 ASN W 82 ASN X 78 ASN ** a 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.7808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 88169 Z= 0.188 Angle : 0.596 9.978 132807 Z= 0.311 Chirality : 0.037 0.295 17116 Planarity : 0.005 0.054 6410 Dihedral : 22.975 179.970 46114 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.27 % Allowed : 27.34 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -1.72 (0.15), residues: 2607 helix: -0.55 (0.21), residues: 641 sheet: -0.28 (0.22), residues: 531 loop : -1.80 (0.14), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 213 HIS 0.006 0.001 HIS E 60 PHE 0.014 0.002 PHE A 76 TYR 0.019 0.002 TYR Y 74 ARG 0.006 0.000 ARG a 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 315 time to evaluate : 3.435 Fit side-chains revert: symmetry clash REVERT: A 87 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6618 (mt-10) REVERT: A 90 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6067 (ppp80) REVERT: C 19 LYS cc_start: 0.8234 (tttt) cc_final: 0.8033 (tppt) REVERT: C 49 ASP cc_start: 0.8434 (m-30) cc_final: 0.7893 (m-30) REVERT: D 37 LYS cc_start: 0.6814 (mtpm) cc_final: 0.6110 (tttt) REVERT: F 14 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6463 (mt-10) REVERT: G 4 LYS cc_start: 0.7966 (tttm) cc_final: 0.7665 (tttt) REVERT: G 41 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.5986 (mmm) REVERT: K 21 SER cc_start: 0.7385 (OUTLIER) cc_final: 0.7075 (p) REVERT: K 29 ARG cc_start: 0.7593 (mtt-85) cc_final: 0.6962 (mtm110) REVERT: N 17 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.6746 (mtp180) REVERT: O 1 MET cc_start: 0.5438 (ttp) cc_final: 0.5143 (ptp) REVERT: P 30 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7557 (tttt) REVERT: V 102 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8483 (mm) REVERT: W 53 LYS cc_start: 0.7682 (mtpt) cc_final: 0.7400 (mtpt) REVERT: Z 34 GLU cc_start: 0.7559 (tp30) cc_final: 0.7096 (tp30) REVERT: Z 89 ILE cc_start: 0.8517 (mm) cc_final: 0.8217 (mp) REVERT: a 4 LYS cc_start: 0.5654 (OUTLIER) cc_final: 0.5048 (ptmt) outliers start: 95 outliers final: 62 residues processed: 372 average time/residue: 1.5789 time to fit residues: 796.2272 Evaluate side-chains 383 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 312 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain P residue 30 LYS Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 125 VAL Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 52 ILE Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain a residue 4 LYS Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 469 optimal weight: 9.9990 chunk 494 optimal weight: 8.9990 chunk 451 optimal weight: 7.9990 chunk 481 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 378 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 435 optimal weight: 10.0000 chunk 455 optimal weight: 10.0000 chunk 479 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN E 60 HIS L 187 GLN Q 43 GLN V 41 ASN W 82 ASN ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.7978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.140 88169 Z= 0.581 Angle : 0.985 10.788 132807 Z= 0.482 Chirality : 0.054 0.385 17116 Planarity : 0.007 0.074 6410 Dihedral : 23.377 177.727 46114 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 5.80 % Allowed : 25.94 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.19 (0.14), residues: 2607 helix: -1.02 (0.20), residues: 634 sheet: -0.57 (0.21), residues: 541 loop : -2.06 (0.13), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 250 HIS 0.010 0.002 HIS N 19 PHE 0.028 0.003 PHE C 25 TYR 0.026 0.003 TYR V 126 ARG 0.008 0.001 ARG a 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 299 time to evaluate : 3.278 Fit side-chains revert: symmetry clash REVERT: A 87 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6732 (mt-10) REVERT: A 90 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6442 (ppp80) REVERT: B 65 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8277 (mm) REVERT: B 87 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7485 (mtt-85) REVERT: B 255 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8246 (mp) REVERT: C 19 LYS cc_start: 0.8372 (tttt) cc_final: 0.8105 (tppt) REVERT: C 49 ASP cc_start: 0.8476 (m-30) cc_final: 0.8075 (m-30) REVERT: F 14 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6475 (mt-10) REVERT: G 41 MET cc_start: 0.6482 (OUTLIER) cc_final: 0.5940 (mmm) REVERT: H 12 LYS cc_start: 0.5211 (OUTLIER) cc_final: 0.4895 (tttm) REVERT: K 21 SER cc_start: 0.7684 (OUTLIER) cc_final: 0.7246 (p) REVERT: K 29 ARG cc_start: 0.7648 (mtt-85) cc_final: 0.6977 (mtm110) REVERT: L 100 GLU cc_start: 0.6682 (mm-30) cc_final: 0.6450 (mm-30) REVERT: N 17 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.6818 (mtp180) REVERT: P 30 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7630 (tttt) REVERT: P 34 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7922 (mtm-85) REVERT: R 2 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8147 (mtpt) REVERT: V 102 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8504 (mm) REVERT: W 53 LYS cc_start: 0.7770 (mtpt) cc_final: 0.7453 (mtpt) REVERT: X 15 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6558 (mt-10) REVERT: Y 6 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7006 (ttm170) REVERT: Y 79 LEU cc_start: 0.7550 (mt) cc_final: 0.7288 (mp) REVERT: Z 89 ILE cc_start: 0.8619 (mm) cc_final: 0.8317 (mp) outliers start: 129 outliers final: 92 residues processed: 385 average time/residue: 1.6356 time to fit residues: 847.4101 Evaluate side-chains 405 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 297 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain P residue 30 LYS Chi-restraints excluded: chain P residue 34 ARG Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain Q residue 31 HIS Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 2 LYS Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 125 VAL Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 66 LYS Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 15 GLU Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Y residue 52 ILE Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain a residue 4 LYS Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 316 optimal weight: 2.9990 chunk 509 optimal weight: 7.9990 chunk 310 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 353 optimal weight: 3.9990 chunk 533 optimal weight: 9.9990 chunk 491 optimal weight: 6.9990 chunk 425 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 328 optimal weight: 4.9990 chunk 260 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN B 114 GLN B 133 GLN E 60 HIS G 8 ASN L 187 GLN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 41 ASN W 82 ASN ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.7916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 88169 Z= 0.302 Angle : 0.699 10.764 132807 Z= 0.357 Chirality : 0.042 0.326 17116 Planarity : 0.006 0.054 6410 Dihedral : 23.097 177.905 46114 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.45 % Allowed : 27.52 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -1.95 (0.15), residues: 2607 helix: -0.74 (0.20), residues: 638 sheet: -0.39 (0.22), residues: 540 loop : -1.97 (0.13), residues: 1429 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 0.018 0.002 PHE C 25 TYR 0.020 0.002 TYR Y 74 ARG 0.007 0.001 ARG a 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 312 time to evaluate : 3.354 Fit side-chains revert: symmetry clash REVERT: A 87 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6693 (mt-10) REVERT: A 90 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6177 (ppp80) REVERT: B 65 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8431 (mm) REVERT: B 87 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7691 (mtm-85) REVERT: C 19 LYS cc_start: 0.8254 (tttt) cc_final: 0.8015 (tppt) REVERT: C 49 ASP cc_start: 0.8419 (m-30) cc_final: 0.7908 (m-30) REVERT: F 14 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6477 (mt-10) REVERT: G 4 LYS cc_start: 0.8081 (tttm) cc_final: 0.7756 (tttt) REVERT: G 41 MET cc_start: 0.6489 (OUTLIER) cc_final: 0.5988 (mmm) REVERT: K 21 SER cc_start: 0.7477 (OUTLIER) cc_final: 0.7148 (p) REVERT: K 29 ARG cc_start: 0.7614 (mtt-85) cc_final: 0.6970 (mtm110) REVERT: L 100 GLU cc_start: 0.6520 (mm-30) cc_final: 0.6315 (mm-30) REVERT: N 17 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.6795 (mtp180) REVERT: O 1 MET cc_start: 0.5456 (ttp) cc_final: 0.5212 (ptp) REVERT: P 30 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7586 (tttt) REVERT: P 34 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7917 (mtm-85) REVERT: V 102 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8484 (mm) REVERT: W 53 LYS cc_start: 0.7724 (mtpt) cc_final: 0.7423 (mtpt) REVERT: X 15 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6525 (mt-10) REVERT: Y 1 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6680 (mtt) REVERT: Y 6 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7009 (ttm170) REVERT: Y 31 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: Y 79 LEU cc_start: 0.7528 (mt) cc_final: 0.7296 (mp) REVERT: Z 53 LYS cc_start: 0.7690 (mptt) cc_final: 0.7307 (ttmt) REVERT: Z 89 ILE cc_start: 0.8557 (mm) cc_final: 0.8244 (mp) REVERT: a 4 LYS cc_start: 0.5710 (OUTLIER) cc_final: 0.5053 (ptmt) outliers start: 99 outliers final: 74 residues processed: 374 average time/residue: 1.6553 time to fit residues: 831.3945 Evaluate side-chains 401 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 311 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain N residue 17 ARG Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain P residue 30 LYS Chi-restraints excluded: chain P residue 34 ARG Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 125 VAL Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 15 GLU Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Y residue 31 GLU Chi-restraints excluded: chain Y residue 52 ILE Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain a residue 4 LYS Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 337 optimal weight: 6.9990 chunk 452 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 392 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 118 optimal weight: 0.4980 chunk 425 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 437 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN B 133 GLN E 60 HIS G 8 ASN L 187 GLN Q 43 GLN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 41 ASN W 82 ASN ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 97 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.149014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.126163 restraints weight = 95743.443| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 0.91 r_work: 0.3037 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.7916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 88169 Z= 0.280 Angle : 0.685 10.795 132807 Z= 0.352 Chirality : 0.041 0.321 17116 Planarity : 0.005 0.053 6410 Dihedral : 23.096 177.795 46114 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.22 % Allowed : 26.93 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -1.89 (0.15), residues: 2607 helix: -0.65 (0.20), residues: 638 sheet: -0.39 (0.22), residues: 534 loop : -1.93 (0.13), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 213 HIS 0.007 0.001 HIS C 29 PHE 0.016 0.002 PHE C 25 TYR 0.021 0.002 TYR Y 74 ARG 0.008 0.001 ARG a 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15554.67 seconds wall clock time: 275 minutes 38.80 seconds (16538.80 seconds total)