Starting phenix.real_space_refine on Mon Feb 19 18:26:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttw_26125/02_2024/7ttw_26125.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttw_26125/02_2024/7ttw_26125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttw_26125/02_2024/7ttw_26125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttw_26125/02_2024/7ttw_26125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttw_26125/02_2024/7ttw_26125.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttw_26125/02_2024/7ttw_26125.pdb" } resolution = 2.9 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 2791 5.49 5 S 56 5.16 5 C 39822 2.51 5 N 15008 2.21 5 O 23176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "G GLU 36": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "L GLU 29": "OE1" <-> "OE2" Residue "L GLU 74": "OE1" <-> "OE2" Residue "L GLU 210": "OE1" <-> "OE2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "S GLU 164": "OE1" <-> "OE2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "X GLU 10": "OE1" <-> "OE2" Residue "Y GLU 112": "OE1" <-> "OE2" Residue "Z GLU 28": "OE1" <-> "OE2" Residue "Z GLU 91": "OE1" <-> "OE2" Residue "Z GLU 95": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 80853 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: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1635 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: 57665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2690, 57665 Inner-chain residues flagged as termini: ['pdbres=" G 1 291 "', 'pdbres=" A 1 318 "', 'pdbres=" A 11092 "', 'pdbres=" G 11154 "', 'pdbres=" A 11459 "', 'pdbres=" G 11556 "', 'pdbres=" C 11587 "', 'pdbres=" G 12217 "'] Classifications: {'RNA': 2690} Modifications used: {'5*END': 9, 'rna2p_pur': 269, 'rna2p_pyr': 137, 'rna3p_pur': 1278, 'rna3p_pyr': 1006} Link IDs: {'rna2p': 406, 'rna3p': 2283} Chain breaks: 2 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: 32.17, per 1000 atoms: 0.40 Number of scatterers: 80853 At special positions: 0 Unit cell: (212.115, 237.175, 187.95, 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 56 16.00 P 2791 15.00 O 23176 8.00 N 15008 7.00 C 39822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 43 " distance=2.04 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS R 27 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 32.42 Conformation dependent library (CDL) restraints added in 3.8 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: 4842 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 41 sheets defined 26.0% alpha, 21.1% beta 700 base pairs and 1439 stacking pairs defined. Time for finding SS restraints: 27.37 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.572A pdb=" N ALA A 110 " --> pdb=" O GLY A 107 " (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: 4.403A pdb=" N GLU B 201 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 203 " --> pdb=" O HIS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 213 removed outlier: 3.851A pdb=" N SER B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.582A pdb=" N VAL B 224 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 3.708A 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 'C' and resid 9 through 20 removed outlier: 3.517A pdb=" N ARG C 13 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.533A pdb=" N HIS C 29 " --> pdb=" O GLY C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 71 removed outlier: 4.014A pdb=" N ARG C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG C 55 " --> pdb=" O ARG C 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C 58 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 87 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.544A pdb=" N SER C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 removed outlier: 3.725A pdb=" N ALA C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 108 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS C 112 " --> pdb=" O GLN C 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 25 removed outlier: 4.329A pdb=" N LEU E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE E 24 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 removed outlier: 3.575A pdb=" N ALA E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 61 removed outlier: 3.607A pdb=" N VAL E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) 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 Processing helix chain 'F' and resid 34 through 47 removed outlier: 3.630A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 24 removed outlier: 3.538A pdb=" N GLN H 20 " --> pdb=" O SER H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 56 removed outlier: 3.727A pdb=" N LYS H 50 " --> pdb=" O VAL H 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 55 removed outlier: 3.588A pdb=" N LYS J 55 " --> pdb=" O ARG J 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 52 through 55' Processing helix chain 'K' and resid 9 through 23 removed outlier: 4.437A pdb=" N GLU K 15 " --> pdb=" O THR K 11 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE K 18 " --> pdb=" O ILE K 14 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER K 21 " --> pdb=" O GLN K 17 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU K 23 " --> pdb=" O LYS K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 35 removed outlier: 3.660A pdb=" N GLN K 31 " --> pdb=" O ASN K 27 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU K 32 " --> pdb=" O LEU K 28 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA K 33 " --> pdb=" O ARG K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 60 removed outlier: 3.518A pdb=" N ARG K 60 " --> pdb=" O VAL K 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 80 removed outlier: 3.630A pdb=" N GLY L 75 " --> pdb=" O LYS L 71 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS L 76 " --> pdb=" O PRO L 72 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA L 80 " --> pdb=" O HIS L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'L' and resid 106 through 110 Processing helix chain 'L' and resid 129 through 135 Processing helix chain 'M' and resid 16 through 27 removed outlier: 3.988A pdb=" N THR M 22 " --> pdb=" O THR M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 48 removed outlier: 3.772A pdb=" N GLN M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 17 Processing helix chain 'P' and resid 9 through 18 Processing helix chain 'P' and resid 18 through 24 Processing helix chain 'P' and resid 25 through 38 removed outlier: 3.599A pdb=" N VAL P 31 " --> pdb=" O ASN P 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 12 removed outlier: 3.565A pdb=" N LYS Q 12 " --> pdb=" O ARG Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 36 Processing helix chain 'Q' and resid 37 through 44 Processing helix chain 'Q' and resid 51 through 59 removed outlier: 4.312A pdb=" N ARG Q 57 " --> pdb=" O SER Q 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 33 removed outlier: 4.027A pdb=" N LYS R 33 " --> pdb=" O PRO R 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 43 Processing helix chain 'S' and resid 102 through 120 removed outlier: 3.868A pdb=" N LEU S 110 " --> pdb=" O ARG S 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 146 removed outlier: 3.721A pdb=" N PHE S 139 " --> pdb=" O LYS S 135 " (cutoff:3.500A) Processing helix chain 'S' and resid 160 through 166 removed outlier: 4.188A pdb=" N SER S 166 " --> pdb=" O ASN S 162 " (cutoff:3.500A) Processing helix chain 'S' and resid 177 through 181 removed outlier: 3.587A pdb=" N GLY S 180 " --> pdb=" O THR S 177 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU S 181 " --> pdb=" O ALA S 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 177 through 181' Processing helix chain 'S' and resid 182 through 189 Processing helix chain 'S' and resid 196 through 206 Processing helix chain 'V' and resid 25 through 39 removed outlier: 3.924A pdb=" N GLU V 32 " --> pdb=" O ARG V 28 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER V 35 " --> pdb=" O SER V 31 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE V 36 " --> pdb=" O GLU V 32 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY V 39 " --> pdb=" O SER V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 73 Processing helix chain 'V' and resid 90 through 94 Processing helix chain 'V' and resid 97 through 108 Processing helix chain 'V' and resid 113 through 120 removed outlier: 3.594A pdb=" N LYS V 118 " --> pdb=" O ARG V 114 " (cutoff:3.500A) Processing helix chain 'W' and resid 103 through 107 removed outlier: 3.802A pdb=" N LEU W 106 " --> pdb=" O ALA W 103 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG W 107 " --> pdb=" O ARG W 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 103 through 107' Processing helix chain 'W' and resid 111 through 118 removed outlier: 3.763A pdb=" N LEU W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA W 118 " --> pdb=" O ILE W 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 80 through 83 Processing helix chain 'X' and resid 92 through 97 removed outlier: 3.780A pdb=" N VAL X 97 " --> pdb=" O PRO X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 129 through 139 removed outlier: 3.797A pdb=" N LYS X 139 " --> pdb=" O ALA X 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 56 removed outlier: 3.758A pdb=" N MET Y 54 " --> pdb=" O ALA Y 50 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG Y 56 " --> pdb=" O ILE Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 110 through 123 removed outlier: 3.719A pdb=" N HIS Y 123 " --> pdb=" O ARG Y 119 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 28 Processing helix chain 'Z' and resid 34 through 52 removed outlier: 3.813A pdb=" N GLU Z 39 " --> pdb=" O ALA Z 35 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER Z 42 " --> pdb=" O LYS Z 38 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL Z 43 " --> pdb=" O GLU Z 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 63 Processing helix chain 'Z' and resid 81 through 88 Processing helix chain 'Z' and resid 89 through 93 removed outlier: 3.722A pdb=" N TYR Z 93 " --> pdb=" O ALA Z 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 17 removed outlier: 3.627A pdb=" N VAL a 10 " --> pdb=" O ASP a 6 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU a 12 " --> pdb=" O ASN a 8 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS a 13 " --> pdb=" O LYS a 9 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG a 17 " --> pdb=" O LYS a 13 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 87 removed outlier: 3.920A pdb=" N GLU a 78 " --> pdb=" O THR a 74 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA a 81 " --> pdb=" O GLY a 77 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS a 83 " --> pdb=" O ALA a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 115 removed outlier: 3.500A pdb=" N ALA a 111 " --> pdb=" O ALA a 107 " (cutoff:3.500A) removed outlier: 3.526A 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 91 removed outlier: 7.132A pdb=" N HIS A 31 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE A 86 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG A 29 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL A 88 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR A 27 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP A 26 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N GLU A 46 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE A 66 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A 62 " --> pdb=" O ILE A 50 " (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 36 Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 105 removed outlier: 6.670A pdb=" N ILE B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE B 81 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.771A 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: 6.601A pdb=" N LEU B 173 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS B 167 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL B 181 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 144 through 145 removed outlier: 6.262A pdb=" N ILE B 144 " --> pdb=" O GLN B 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.486A pdb=" N ILE D 4 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 19 through 23 removed outlier: 5.951A pdb=" N ILE D 97 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR D 61 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS D 99 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 77 removed outlier: 3.509A pdb=" N THR D 75 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER D 82 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 10 removed outlier: 3.520A pdb=" N THR E 9 " --> pdb=" O SER E 101 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER E 101 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N SER E 108 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.607A 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: 6.551A pdb=" N ASP F 28 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N THR F 26 " --> pdb=" O PRO F 10 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG F 76 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG F 75 " --> pdb=" O TYR F 58 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LYS F 83 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL F 50 " --> pdb=" O LYS F 83 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 62 through 65 removed outlier: 3.644A pdb=" N TYR F 68 " --> pdb=" O MET F 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 9 through 11 removed outlier: 4.164A pdb=" N LEU G 70 " --> pdb=" O THR G 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 23 through 27 removed outlier: 6.902A pdb=" N VAL G 34 " --> pdb=" O ILE G 24 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N THR G 26 " --> pdb=" O ARG G 32 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ARG G 32 " --> pdb=" O THR G 26 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 40 through 43 Processing sheet with id=AB8, first strand: chain 'G' and resid 81 through 83 Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 5 removed outlier: 6.975A pdb=" N LEU H 4 " --> pdb=" O GLY H 64 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASP H 90 " --> pdb=" O ALA H 75 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR H 77 " --> pdb=" O HIS H 88 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS H 88 " --> pdb=" O TYR H 77 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE H 79 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE H 86 " --> pdb=" O PHE H 79 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N LYS H 26 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ILE H 89 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N PHE H 91 " --> pdb=" O PRO H 28 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL H 30 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA H 93 " --> pdb=" O VAL H 30 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 30 through 31 removed outlier: 6.784A pdb=" N LEU I 67 " --> pdb=" O LEU I 45 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AC3, first strand: chain 'J' and resid 13 through 18 Processing sheet with id=AC4, first strand: chain 'J' and resid 33 through 37 Processing sheet with id=AC5, first strand: chain 'L' and resid 5 through 16 removed outlier: 6.811A pdb=" N VAL L 27 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N MET L 12 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL L 25 " --> pdb=" O MET L 12 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLN L 14 " --> pdb=" O ILE L 23 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE L 23 " --> pdb=" O GLN L 14 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL L 194 " --> pdb=" O VAL L 188 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL L 188 " --> pdb=" O VAL L 194 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU L 196 " --> pdb=" O VAL L 186 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU L 184 " --> pdb=" O LYS L 198 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N THR L 179 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLY L 120 " --> pdb=" O THR L 179 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLN L 181 " --> pdb=" O VAL L 118 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL L 118 " --> pdb=" O GLN L 181 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL L 121 " --> pdb=" O LEU L 208 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU L 208 " --> pdb=" O VAL L 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 88 through 91 removed outlier: 3.534A pdb=" N ILE L 49 " --> pdb=" O PHE L 91 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN L 37 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY L 52 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL L 35 " --> pdb=" O GLY L 52 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN L 33 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 124 through 128 removed outlier: 3.613A pdb=" N GLY L 126 " --> pdb=" O MET L 173 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 34 through 38 Processing sheet with id=AC9, first strand: chain 'N' and resid 27 through 29 Processing sheet with id=AD1, first strand: chain 'O' and resid 17 through 22 removed outlier: 3.769A pdb=" N LYS O 41 " --> pdb=" O CYS O 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 15 through 16 Processing sheet with id=AD3, first strand: chain 'R' and resid 16 through 19 Processing sheet with id=AD4, first strand: chain 'S' and resid 123 through 126 removed outlier: 6.198A pdb=" N THR S 124 " --> pdb=" O ILE S 194 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU S 153 " --> pdb=" O VAL S 193 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N THR S 195 " --> pdb=" O LEU S 153 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL S 155 " --> pdb=" O THR S 195 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL S 152 " --> pdb=" O GLN S 174 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N THR S 176 " --> pdb=" O VAL S 152 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL S 154 " --> pdb=" O THR S 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'V' and resid 123 through 125 Processing sheet with id=AD6, first strand: chain 'V' and resid 74 through 78 Processing sheet with id=AD7, first strand: chain 'W' and resid 7 through 10 removed outlier: 6.059A pdb=" N ARG W 17 " --> pdb=" O VAL W 10 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN W 45 " --> pdb=" O ARG W 17 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL W 19 " --> pdb=" O VAL W 43 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL W 43 " --> pdb=" O VAL W 19 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR W 21 " --> pdb=" O CYS W 41 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N CYS W 41 " --> pdb=" O THR W 21 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS W 23 " --> pdb=" O ILE W 39 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE W 39 " --> pdb=" O LYS W 23 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA W 83 " --> pdb=" O VAL W 63 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N CYS W 84 " --> pdb=" O ARG W 7 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS W 9 " --> pdb=" O CYS W 84 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE W 86 " --> pdb=" O LYS W 9 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 75 through 78 removed outlier: 6.073A pdb=" N ALA X 75 " --> pdb=" O LYS X 110 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU X 112 " --> pdb=" O ALA X 75 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL X 77 " --> pdb=" O LEU X 112 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE X 109 " --> pdb=" O LYS X 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'X' and resid 90 through 91 removed outlier: 7.600A pdb=" N VAL X 123 " --> pdb=" O GLU X 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 63 through 66 removed outlier: 6.633A pdb=" N ILE Y 102 " --> pdb=" O ALA Y 36 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA Y 36 " --> pdb=" O ILE Y 102 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE Y 104 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Y' and resid 40 through 43 removed outlier: 5.759A pdb=" N VAL Y 90 " --> pdb=" O LYS Y 76 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LYS Y 76 " --> pdb=" O VAL Y 90 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY Y 92 " --> pdb=" O TYR Y 74 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Z' and resid 29 through 33 removed outlier: 6.282A pdb=" N SER Z 116 " --> pdb=" O GLN Z 106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Z' and resid 70 through 71 removed outlier: 3.535A pdb=" N GLN Z 79 " --> pdb=" O ILE Z 71 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'a' and resid 51 through 57 removed outlier: 6.801A pdb=" N ILE a 44 " --> pdb=" O LEU a 53 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLN a 55 " --> pdb=" O ALA a 42 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ALA a 42 " --> pdb=" O GLN a 55 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N SER a 57 " --> pdb=" O ILE a 40 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE a 40 " --> pdb=" O SER a 57 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1747 hydrogen bonds 2802 hydrogen bond angles 0 basepair planarities 700 basepair parallelities 1439 stacking parallelities Total time for adding SS restraints: 110.32 Time building geometry restraints manager: 35.06 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: 12030 1.33 - 1.46: 39246 1.46 - 1.58: 31355 1.58 - 1.70: 5580 1.70 - 1.83: 98 Bond restraints: 88309 Sorted by residual: bond pdb=" N MET S 101 " pdb=" CA MET S 101 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.44e+01 bond pdb=" O3' A 1 329 " pdb=" P C 1 330 " ideal model delta sigma weight residual 1.607 1.649 -0.042 1.50e-02 4.44e+03 7.90e+00 bond pdb=" N VAL H 55 " pdb=" CA VAL H 55 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.29e-02 6.01e+03 7.39e+00 bond pdb=" N ASN H 58 " pdb=" CA ASN H 58 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.16e-02 7.43e+03 7.29e+00 bond pdb=" N GLU H 54 " pdb=" CA GLU H 54 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.87e+00 ... (remaining 88304 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.47: 16777 106.47 - 113.35: 51914 113.35 - 120.23: 31562 120.23 - 127.11: 26139 127.11 - 134.00: 6630 Bond angle restraints: 133022 Sorted by residual: angle pdb=" N ASN N 32 " pdb=" CA ASN N 32 " pdb=" C ASN N 32 " ideal model delta sigma weight residual 113.18 106.54 6.64 1.33e+00 5.65e-01 2.49e+01 angle pdb=" O3' A 11488 " pdb=" C3' A 11488 " pdb=" C2' A 11488 " ideal model delta sigma weight residual 113.70 107.99 5.71 1.50e+00 4.44e-01 1.45e+01 angle pdb=" O4' A 11489 " pdb=" C1' A 11489 " pdb=" C2' A 11489 " ideal model delta sigma weight residual 105.80 102.03 3.77 1.00e+00 1.00e+00 1.42e+01 angle pdb=" CA MET S 101 " pdb=" C MET S 101 " pdb=" N PRO S 102 " ideal model delta sigma weight residual 117.71 121.12 -3.41 9.20e-01 1.18e+00 1.38e+01 angle pdb=" N MET S 105 " pdb=" CA MET S 105 " pdb=" C MET S 105 " ideal model delta sigma weight residual 113.23 108.66 4.57 1.24e+00 6.50e-01 1.36e+01 ... (remaining 133017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 50042 35.93 - 71.86: 5717 71.86 - 107.79: 641 107.79 - 143.72: 11 143.72 - 179.65: 39 Dihedral angle restraints: 56450 sinusoidal: 48916 harmonic: 7534 Sorted by residual: dihedral pdb=" O4' U 11545 " pdb=" C1' U 11545 " pdb=" N1 U 11545 " pdb=" C2 U 11545 " ideal model delta sinusoidal sigma weight residual 200.00 21.85 178.15 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 1 556 " pdb=" C1' U 1 556 " pdb=" N1 U 1 556 " pdb=" C2 U 1 556 " ideal model delta sinusoidal sigma weight residual -160.00 16.96 -176.96 1 1.50e+01 4.44e-03 8.53e+01 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 200.00 23.33 176.67 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 56447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 15466 0.055 - 0.109: 1402 0.109 - 0.164: 238 0.164 - 0.219: 36 0.219 - 0.274: 7 Chirality restraints: 17149 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 2.19 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1' A 11024 " pdb=" O4' A 11024 " pdb=" C2' A 11024 " pdb=" N9 A 11024 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C1' A 1 125 " pdb=" O4' A 1 125 " pdb=" C2' A 1 125 " pdb=" N9 A 1 125 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 17146 not shown) Planarity restraints: 6417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 1 661 " 0.038 2.00e-02 2.50e+03 2.04e-02 9.37e+00 pdb=" N1 U 1 661 " -0.045 2.00e-02 2.50e+03 pdb=" C2 U 1 661 " -0.004 2.00e-02 2.50e+03 pdb=" O2 U 1 661 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U 1 661 " 0.006 2.00e-02 2.50e+03 pdb=" C4 U 1 661 " 0.010 2.00e-02 2.50e+03 pdb=" O4 U 1 661 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U 1 661 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U 1 661 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11024 " 0.037 2.00e-02 2.50e+03 1.65e-02 7.51e+00 pdb=" N9 A 11024 " -0.038 2.00e-02 2.50e+03 pdb=" C8 A 11024 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A 11024 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A 11024 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A 11024 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A 11024 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A 11024 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A 11024 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A 11024 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A 11024 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11489 " 0.033 2.00e-02 2.50e+03 1.61e-02 7.16e+00 pdb=" N9 A 11489 " -0.039 2.00e-02 2.50e+03 pdb=" C8 A 11489 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A 11489 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A 11489 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A 11489 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A 11489 " 0.002 2.00e-02 2.50e+03 pdb=" N1 A 11489 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A 11489 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A 11489 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A 11489 " -0.003 2.00e-02 2.50e+03 ... (remaining 6414 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 1533 2.63 - 3.20: 59925 3.20 - 3.77: 146511 3.77 - 4.33: 213921 4.33 - 4.90: 281768 Nonbonded interactions: 703658 Sorted by model distance: nonbonded pdb=" O2' G 12432 " pdb=" OP2 C 12433 " model vdw 2.065 2.440 nonbonded pdb=" O2' G 12007 " pdb=" OP2 U 12009 " model vdw 2.094 2.440 nonbonded pdb=" OP2 U 1 89 " pdb=" O2' A 1 90 " model vdw 2.104 2.440 nonbonded pdb=" OD1 ASP Z 112 " pdb=" O2' G 11693 " model vdw 2.148 2.440 nonbonded pdb=" O2' A 11939 " pdb=" OP2 C 11941 " model vdw 2.150 2.440 ... (remaining 703653 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: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.080 Extract box with map and model: 18.550 Check model and map are aligned: 0.930 Set scattering table: 0.580 Process input model: 262.350 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 299.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 88309 Z= 0.156 Angle : 0.539 10.326 133022 Z= 0.291 Chirality : 0.035 0.274 17149 Planarity : 0.004 0.054 6417 Dihedral : 22.866 179.652 51602 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.04 % Allowed : 0.40 % Favored : 99.55 % 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: -2.03 (0.15), residues: 2607 helix: -1.77 (0.19), residues: 594 sheet: -0.43 (0.22), residues: 544 loop : -1.52 (0.14), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 213 HIS 0.007 0.001 HIS Q 31 PHE 0.013 0.001 PHE K 30 TYR 0.012 0.001 TYR V 126 ARG 0.007 0.000 ARG E 92 *********************** 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 370 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 369 time to evaluate : 3.443 Fit side-chains REVERT: H 78 GLN cc_start: 0.7445 (mt0) cc_final: 0.7006 (mp10) REVERT: L 61 LYS cc_start: 0.7032 (tptp) cc_final: 0.6423 (tmtp) REVERT: L 70 ASN cc_start: 0.8373 (p0) cc_final: 0.8117 (p0) REVERT: O 18 ILE cc_start: 0.7903 (pt) cc_final: 0.7674 (pt) REVERT: S 164 GLU cc_start: 0.5884 (tm-30) cc_final: 0.5530 (tm-30) REVERT: V 86 LYS cc_start: 0.7989 (mmtp) cc_final: 0.7761 (mptp) REVERT: X 15 GLU cc_start: 0.7207 (tt0) cc_final: 0.6967 (tt0) REVERT: Y 5 LYS cc_start: 0.7597 (mtmt) cc_final: 0.7371 (mttm) outliers start: 1 outliers final: 0 residues processed: 370 average time/residue: 1.8036 time to fit residues: 870.6484 Evaluate side-chains 324 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 453 optimal weight: 8.9990 chunk 407 optimal weight: 8.9990 chunk 225 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 274 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 chunk 420 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 313 optimal weight: 8.9990 chunk 487 optimal weight: 10.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN E 61 ASN G 8 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN J 23 ASN L 47 ASN L 103 GLN L 192 ASN N 19 HIS X 81 GLN Y 35 GLN Z 106 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 88309 Z= 0.475 Angle : 0.965 14.676 133022 Z= 0.475 Chirality : 0.052 0.380 17149 Planarity : 0.008 0.102 6417 Dihedral : 23.482 179.953 46224 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.52 % Allowed : 10.16 % Favored : 87.33 % 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: -2.15 (0.15), residues: 2607 helix: -1.19 (0.19), residues: 633 sheet: -0.72 (0.22), residues: 564 loop : -1.86 (0.14), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP B 213 HIS 0.016 0.002 HIS Q 31 PHE 0.030 0.003 PHE X 50 TYR 0.030 0.003 TYR V 126 ARG 0.013 0.001 ARG B 43 *********************** 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 392 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 336 time to evaluate : 3.313 Fit side-chains REVERT: B 84 ASP cc_start: 0.8431 (t0) cc_final: 0.7328 (t70) REVERT: B 87 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6045 (mtm-85) REVERT: D 47 LYS cc_start: 0.6536 (OUTLIER) cc_final: 0.5949 (mmtt) REVERT: F 9 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6824 (mpp80) REVERT: F 71 TYR cc_start: 0.7970 (m-80) cc_final: 0.7308 (m-80) REVERT: H 78 GLN cc_start: 0.7449 (mt0) cc_final: 0.6960 (mp10) REVERT: L 61 LYS cc_start: 0.7120 (tptp) cc_final: 0.6517 (tmtp) REVERT: L 97 ASP cc_start: 0.6923 (p0) cc_final: 0.6564 (p0) REVERT: S 164 GLU cc_start: 0.5828 (tm-30) cc_final: 0.5536 (tm-30) REVERT: W 67 SER cc_start: 0.8475 (OUTLIER) cc_final: 0.8244 (t) REVERT: W 97 ARG cc_start: 0.6322 (mtp180) cc_final: 0.5847 (mtp85) REVERT: W 107 ARG cc_start: 0.7129 (ptp-170) cc_final: 0.6842 (ptp-170) REVERT: X 15 GLU cc_start: 0.7192 (tt0) cc_final: 0.6917 (tt0) REVERT: X 127 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7406 (mptp) REVERT: Y 5 LYS cc_start: 0.7797 (mtmt) cc_final: 0.7478 (mttm) outliers start: 56 outliers final: 26 residues processed: 366 average time/residue: 1.8517 time to fit residues: 881.1068 Evaluate side-chains 350 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 319 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 110 ASN Chi-restraints excluded: chain X residue 7 LYS Chi-restraints excluded: chain X residue 59 ARG Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain a residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 271 optimal weight: 10.0000 chunk 151 optimal weight: 0.6980 chunk 405 optimal weight: 10.0000 chunk 332 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 488 optimal weight: 7.9990 chunk 527 optimal weight: 10.0000 chunk 435 optimal weight: 10.0000 chunk 484 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 391 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 ASN E 65 ASN G 8 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 ASN L 103 GLN L 192 ASN M 40 ASN Q 31 HIS a 21 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 88309 Z= 0.335 Angle : 0.780 13.198 133022 Z= 0.394 Chirality : 0.044 0.364 17149 Planarity : 0.006 0.086 6417 Dihedral : 23.298 179.492 46224 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.28 % Allowed : 14.34 % Favored : 82.38 % 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: -2.03 (0.15), residues: 2607 helix: -0.80 (0.20), residues: 631 sheet: -0.71 (0.21), residues: 587 loop : -1.92 (0.14), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 213 HIS 0.010 0.002 HIS Q 31 PHE 0.028 0.003 PHE X 50 TYR 0.025 0.002 TYR V 126 ARG 0.009 0.001 ARG E 92 *********************** 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 399 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 326 time to evaluate : 3.571 Fit side-chains REVERT: A 33 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.6037 (mtt180) REVERT: B 84 ASP cc_start: 0.8473 (t0) cc_final: 0.7294 (t70) REVERT: B 87 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.5980 (mtm-85) REVERT: D 47 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.5922 (mmtt) REVERT: E 27 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7791 (mmtp) REVERT: F 62 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7386 (mttm) REVERT: F 71 TYR cc_start: 0.7934 (m-80) cc_final: 0.7234 (m-80) REVERT: H 78 GLN cc_start: 0.7493 (mt0) cc_final: 0.7034 (mp10) REVERT: L 61 LYS cc_start: 0.7065 (tptp) cc_final: 0.6522 (tmtp) REVERT: N 27 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7806 (ptt) REVERT: S 164 GLU cc_start: 0.5772 (tm-30) cc_final: 0.5483 (tm-30) REVERT: W 67 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.8241 (t) REVERT: W 97 ARG cc_start: 0.6350 (mtp180) cc_final: 0.5870 (mtp85) REVERT: W 107 ARG cc_start: 0.7093 (ptp-170) cc_final: 0.6790 (ptp-170) REVERT: X 15 GLU cc_start: 0.7195 (tt0) cc_final: 0.6916 (tt0) REVERT: X 127 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7399 (mptp) REVERT: Y 5 LYS cc_start: 0.7793 (mtmt) cc_final: 0.7473 (mttm) outliers start: 73 outliers final: 35 residues processed: 369 average time/residue: 1.7714 time to fit residues: 868.2150 Evaluate side-chains 356 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 313 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 19 LYS Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain N residue 27 MET Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 110 ASN Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 59 ARG Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 482 optimal weight: 8.9990 chunk 367 optimal weight: 10.0000 chunk 253 optimal weight: 9.9990 chunk 54 optimal weight: 0.3980 chunk 233 optimal weight: 0.8980 chunk 328 optimal weight: 7.9990 chunk 490 optimal weight: 10.0000 chunk 519 optimal weight: 8.9990 chunk 256 optimal weight: 9.9990 chunk 464 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 overall best weight: 4.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN L 47 ASN L 103 GLN M 40 ASN Z 97 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 88309 Z= 0.389 Angle : 0.863 14.469 133022 Z= 0.432 Chirality : 0.048 0.378 17149 Planarity : 0.007 0.088 6417 Dihedral : 23.435 179.713 46224 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.22 % Allowed : 17.17 % Favored : 78.61 % 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: -2.15 (0.15), residues: 2607 helix: -0.86 (0.19), residues: 636 sheet: -0.68 (0.22), residues: 558 loop : -2.05 (0.14), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 213 HIS 0.009 0.002 HIS V 131 PHE 0.027 0.003 PHE X 50 TYR 0.028 0.003 TYR V 126 ARG 0.010 0.001 ARG B 43 *********************** 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 413 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 319 time to evaluate : 3.304 Fit side-chains REVERT: A 33 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6000 (mtt180) REVERT: B 84 ASP cc_start: 0.8479 (t0) cc_final: 0.7370 (t70) REVERT: B 87 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6000 (mtm-85) REVERT: D 47 LYS cc_start: 0.6519 (OUTLIER) cc_final: 0.5948 (mmtt) REVERT: E 27 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7839 (mmtp) REVERT: F 32 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6841 (ptm-80) REVERT: F 62 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7363 (mttm) REVERT: F 71 TYR cc_start: 0.7935 (m-80) cc_final: 0.7332 (m-80) REVERT: H 78 GLN cc_start: 0.7542 (mt0) cc_final: 0.7110 (mp10) REVERT: I 61 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7231 (ttm170) REVERT: L 21 GLU cc_start: 0.6931 (pt0) cc_final: 0.6623 (pt0) REVERT: L 61 LYS cc_start: 0.7083 (tptp) cc_final: 0.6545 (tmtp) REVERT: Q 49 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7669 (mp) REVERT: S 164 GLU cc_start: 0.5777 (tm-30) cc_final: 0.5502 (tm-30) REVERT: W 67 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8291 (t) REVERT: W 97 ARG cc_start: 0.6335 (mtp180) cc_final: 0.5873 (mtp85) REVERT: W 107 ARG cc_start: 0.7079 (ptp-170) cc_final: 0.6836 (ptp-170) REVERT: X 15 GLU cc_start: 0.7181 (tt0) cc_final: 0.6882 (tt0) REVERT: X 127 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7428 (mptp) REVERT: Y 5 LYS cc_start: 0.7808 (mtmt) cc_final: 0.7498 (mttm) REVERT: Y 112 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6731 (mt-10) outliers start: 94 outliers final: 54 residues processed: 380 average time/residue: 1.8125 time to fit residues: 901.3813 Evaluate side-chains 381 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 316 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 19 LYS Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 136 GLN Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 110 ASN Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 7 LYS Chi-restraints excluded: chain X residue 59 ARG Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 112 GLU Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 76 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 432 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 386 optimal weight: 8.9990 chunk 214 optimal weight: 5.9990 chunk 442 optimal weight: 9.9990 chunk 358 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 465 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN G 8 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 ASN L 103 GLN L 167 GLN L 192 ASN O 25 ASN X 143 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.113 88309 Z= 0.456 Angle : 0.940 15.054 133022 Z= 0.465 Chirality : 0.051 0.393 17149 Planarity : 0.008 0.095 6417 Dihedral : 23.516 179.899 46224 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 5.21 % Allowed : 18.97 % Favored : 75.82 % 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: -2.32 (0.14), residues: 2607 helix: -1.02 (0.19), residues: 637 sheet: -0.76 (0.21), residues: 560 loop : -2.15 (0.13), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP B 213 HIS 0.011 0.002 HIS V 131 PHE 0.024 0.003 PHE Q 33 TYR 0.031 0.003 TYR V 126 ARG 0.011 0.001 ARG B 43 *********************** 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 436 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 320 time to evaluate : 4.005 Fit side-chains REVERT: A 33 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6045 (mtt180) REVERT: B 84 ASP cc_start: 0.8457 (t0) cc_final: 0.7337 (t70) REVERT: B 87 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6005 (mtm-85) REVERT: E 27 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7812 (mmtp) REVERT: F 62 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7386 (mttm) REVERT: F 71 TYR cc_start: 0.7977 (m-80) cc_final: 0.7393 (m-80) REVERT: H 78 GLN cc_start: 0.7603 (mt0) cc_final: 0.7191 (mp10) REVERT: I 61 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7207 (ttm170) REVERT: L 61 LYS cc_start: 0.7099 (tptp) cc_final: 0.6563 (tmtp) REVERT: S 164 GLU cc_start: 0.5777 (tm-30) cc_final: 0.5503 (tm-30) REVERT: W 67 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8336 (t) REVERT: W 97 ARG cc_start: 0.6270 (mtp180) cc_final: 0.5860 (mtp85) REVERT: X 15 GLU cc_start: 0.7178 (tt0) cc_final: 0.6915 (tt0) REVERT: X 127 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7433 (mptp) REVERT: Y 5 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7521 (mttm) REVERT: Y 112 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6741 (mt-10) REVERT: Z 31 GLU cc_start: 0.6920 (tt0) cc_final: 0.6407 (tp30) REVERT: Z 75 ASP cc_start: 0.2524 (OUTLIER) cc_final: 0.1594 (m-30) REVERT: a 90 LYS cc_start: 0.6334 (ttmm) cc_final: 0.5901 (ttpp) outliers start: 116 outliers final: 71 residues processed: 403 average time/residue: 1.7993 time to fit residues: 952.7658 Evaluate side-chains 393 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 313 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 19 LYS Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 136 GLN Chi-restraints excluded: chain L residue 169 ILE Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 45 ASN Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 110 ASN Chi-restraints excluded: chain X residue 7 LYS Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 44 SER Chi-restraints excluded: chain Y residue 80 GLU Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 112 GLU Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 75 ASP Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 76 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 174 optimal weight: 2.9990 chunk 467 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 304 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 519 optimal weight: 7.9990 chunk 431 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 171 optimal weight: 0.6980 chunk 272 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 HIS D 65 GLN F 37 GLN G 8 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 ASN L 103 GLN X 143 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 88309 Z= 0.160 Angle : 0.582 11.079 133022 Z= 0.305 Chirality : 0.036 0.300 17149 Planarity : 0.005 0.056 6417 Dihedral : 23.051 179.695 46224 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.55 % Allowed : 21.17 % Favored : 75.28 % 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: -1.75 (0.15), residues: 2607 helix: -0.22 (0.21), residues: 620 sheet: -0.46 (0.22), residues: 561 loop : -1.95 (0.14), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 213 HIS 0.006 0.001 HIS C 29 PHE 0.017 0.001 PHE X 50 TYR 0.015 0.001 TYR V 126 ARG 0.009 0.000 ARG E 92 *********************** 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 421 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 342 time to evaluate : 3.310 Fit side-chains REVERT: E 92 ARG cc_start: 0.7700 (mtt90) cc_final: 0.7466 (mtm180) REVERT: F 62 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7408 (mttm) REVERT: F 71 TYR cc_start: 0.7869 (m-80) cc_final: 0.7269 (m-80) REVERT: G 77 GLU cc_start: 0.5628 (OUTLIER) cc_final: 0.5286 (mm-30) REVERT: H 78 GLN cc_start: 0.7459 (mt0) cc_final: 0.7136 (mp10) REVERT: I 61 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7134 (ttm170) REVERT: L 61 LYS cc_start: 0.7044 (tptp) cc_final: 0.6502 (tmtp) REVERT: S 164 GLU cc_start: 0.5718 (tm-30) cc_final: 0.5263 (tm-30) REVERT: W 97 ARG cc_start: 0.6269 (mtp180) cc_final: 0.5856 (mtp85) REVERT: X 15 GLU cc_start: 0.7177 (tt0) cc_final: 0.6895 (tt0) REVERT: Y 5 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7484 (mttm) REVERT: Y 51 ARG cc_start: 0.7839 (ttp-110) cc_final: 0.7560 (ttp80) REVERT: a 51 VAL cc_start: 0.7152 (OUTLIER) cc_final: 0.6845 (t) outliers start: 79 outliers final: 46 residues processed: 389 average time/residue: 1.7192 time to fit residues: 884.6793 Evaluate side-chains 378 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 328 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain Y residue 80 GLU Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 500 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 296 optimal weight: 9.9990 chunk 379 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 chunk 437 optimal weight: 20.0000 chunk 290 optimal weight: 10.0000 chunk 517 optimal weight: 10.0000 chunk 323 optimal weight: 8.9990 chunk 315 optimal weight: 8.9990 chunk 238 optimal weight: 7.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN G 8 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 ASN L 103 GLN L 167 GLN S 40 GLN X 81 GLN X 143 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.158 88309 Z= 0.665 Angle : 1.198 17.249 133022 Z= 0.576 Chirality : 0.061 0.440 17149 Planarity : 0.009 0.120 6417 Dihedral : 23.754 179.639 46224 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 5.71 % Allowed : 20.04 % Favored : 74.25 % 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: -2.47 (0.14), residues: 2607 helix: -1.18 (0.19), residues: 627 sheet: -0.83 (0.21), residues: 577 loop : -2.26 (0.13), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.005 TRP Y 65 HIS 0.014 0.003 HIS V 131 PHE 0.030 0.004 PHE X 50 TYR 0.040 0.004 TYR V 126 ARG 0.013 0.002 ARG S 72 *********************** 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 444 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 317 time to evaluate : 3.810 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6047 (mtt180) REVERT: F 62 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7412 (mttm) REVERT: F 71 TYR cc_start: 0.8046 (m-80) cc_final: 0.7412 (m-80) REVERT: G 17 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6657 (ttpp) REVERT: G 72 ASP cc_start: 0.6699 (OUTLIER) cc_final: 0.6358 (t0) REVERT: H 78 GLN cc_start: 0.7667 (mt0) cc_final: 0.7235 (mp10) REVERT: I 61 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7254 (ttm170) REVERT: L 21 GLU cc_start: 0.6915 (pt0) cc_final: 0.6590 (pt0) REVERT: L 61 LYS cc_start: 0.7095 (tptp) cc_final: 0.6563 (tmtp) REVERT: Q 62 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8023 (mt) REVERT: S 164 GLU cc_start: 0.5774 (tm-30) cc_final: 0.5517 (tm-30) REVERT: W 31 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6916 (ptpt) REVERT: W 67 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8360 (t) REVERT: W 97 ARG cc_start: 0.6369 (mtp180) cc_final: 0.5937 (mtp85) REVERT: X 15 GLU cc_start: 0.7163 (tt0) cc_final: 0.6878 (tt0) REVERT: X 127 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7417 (mptp) REVERT: Y 5 LYS cc_start: 0.7831 (mtmt) cc_final: 0.7591 (mtmm) REVERT: Y 112 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6739 (mt-10) REVERT: Z 75 ASP cc_start: 0.2491 (OUTLIER) cc_final: 0.1524 (m-30) REVERT: a 27 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5771 (pp20) outliers start: 127 outliers final: 85 residues processed: 412 average time/residue: 1.7657 time to fit residues: 957.6232 Evaluate side-chains 411 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 314 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 190 ASP Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 31 LYS Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 45 ASN Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain W residue 110 ASN Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 44 SER Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 80 GLU Chi-restraints excluded: chain Y residue 81 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 112 GLU Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 75 ASP Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 27 GLU Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 320 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 309 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 352 optimal weight: 2.9990 chunk 255 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 406 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN G 8 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 ASN L 103 GLN L 192 ASN X 143 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 88309 Z= 0.184 Angle : 0.616 11.740 133022 Z= 0.322 Chirality : 0.038 0.315 17149 Planarity : 0.005 0.056 6417 Dihedral : 23.127 179.989 46224 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.00 % Allowed : 22.65 % Favored : 73.35 % 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: -1.87 (0.15), residues: 2607 helix: -0.36 (0.20), residues: 621 sheet: -0.56 (0.21), residues: 564 loop : -1.99 (0.14), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 213 HIS 0.005 0.001 HIS C 29 PHE 0.016 0.002 PHE H 79 TYR 0.018 0.002 TYR V 126 ARG 0.009 0.000 ARG E 92 *********************** 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 421 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 332 time to evaluate : 3.385 Fit side-chains REVERT: E 27 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7470 (mmtp) REVERT: F 62 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7360 (mttm) REVERT: F 71 TYR cc_start: 0.7882 (m-80) cc_final: 0.7259 (m-80) REVERT: H 78 GLN cc_start: 0.7606 (mt0) cc_final: 0.7245 (mp10) REVERT: I 61 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7177 (ttm170) REVERT: L 21 GLU cc_start: 0.6885 (pt0) cc_final: 0.6575 (pt0) REVERT: L 61 LYS cc_start: 0.7029 (tptp) cc_final: 0.6500 (tmtp) REVERT: Q 62 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7361 (mt) REVERT: S 164 GLU cc_start: 0.5706 (tm-30) cc_final: 0.5424 (tm-30) REVERT: W 67 SER cc_start: 0.8458 (OUTLIER) cc_final: 0.8213 (t) REVERT: W 97 ARG cc_start: 0.6243 (mtp180) cc_final: 0.5813 (mtp85) REVERT: X 15 GLU cc_start: 0.7172 (tt0) cc_final: 0.6880 (tt0) REVERT: Y 5 LYS cc_start: 0.7804 (mtmt) cc_final: 0.7478 (mttm) REVERT: Y 51 ARG cc_start: 0.7934 (ttp-110) cc_final: 0.7570 (ttp80) outliers start: 89 outliers final: 53 residues processed: 393 average time/residue: 1.6991 time to fit residues: 886.0857 Evaluate side-chains 381 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 323 time to evaluate : 3.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain Y residue 44 SER Chi-restraints excluded: chain Y residue 80 GLU Chi-restraints excluded: chain Y residue 81 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 470 optimal weight: 10.0000 chunk 495 optimal weight: 9.9990 chunk 452 optimal weight: 7.9990 chunk 482 optimal weight: 8.9990 chunk 290 optimal weight: 10.0000 chunk 210 optimal weight: 0.0570 chunk 378 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 chunk 435 optimal weight: 10.0000 chunk 456 optimal weight: 10.0000 chunk 480 optimal weight: 8.9990 overall best weight: 5.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN G 8 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 ASN L 103 GLN L 167 GLN X 81 GLN X 143 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 88309 Z= 0.431 Angle : 0.912 15.110 133022 Z= 0.453 Chirality : 0.050 0.388 17149 Planarity : 0.007 0.094 6417 Dihedral : 23.447 179.976 46224 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.27 % Allowed : 22.61 % Favored : 73.12 % 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: -2.15 (0.15), residues: 2607 helix: -0.74 (0.20), residues: 628 sheet: -0.67 (0.21), residues: 593 loop : -2.15 (0.14), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP Y 65 HIS 0.010 0.002 HIS V 131 PHE 0.023 0.003 PHE Q 33 TYR 0.030 0.003 TYR V 126 ARG 0.009 0.001 ARG E 92 *********************** 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 411 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 316 time to evaluate : 3.329 Fit side-chains REVERT: A 33 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6063 (mtt180) REVERT: F 62 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7394 (mttm) REVERT: F 71 TYR cc_start: 0.7978 (m-80) cc_final: 0.7401 (m-80) REVERT: G 17 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6615 (ttpp) REVERT: G 72 ASP cc_start: 0.6477 (OUTLIER) cc_final: 0.6157 (t0) REVERT: H 78 GLN cc_start: 0.7618 (mt0) cc_final: 0.7136 (mp10) REVERT: I 61 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7241 (ttm170) REVERT: L 61 LYS cc_start: 0.7066 (tptp) cc_final: 0.6533 (tmtp) REVERT: Q 62 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7861 (mt) REVERT: S 164 GLU cc_start: 0.5783 (tm-30) cc_final: 0.5503 (tm-30) REVERT: W 67 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.8315 (t) REVERT: W 97 ARG cc_start: 0.6250 (mtp180) cc_final: 0.5823 (mtp85) REVERT: X 15 GLU cc_start: 0.7180 (tt0) cc_final: 0.6900 (tt0) REVERT: Y 5 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7514 (mttm) REVERT: a 27 GLU cc_start: 0.5956 (OUTLIER) cc_final: 0.5645 (pp20) REVERT: a 90 LYS cc_start: 0.6509 (ttmm) cc_final: 0.5971 (ttpp) outliers start: 95 outliers final: 66 residues processed: 386 average time/residue: 1.7149 time to fit residues: 878.0172 Evaluate side-chains 395 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 321 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 110 ASN Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain Y residue 44 SER Chi-restraints excluded: chain Y residue 80 GLU Chi-restraints excluded: chain Y residue 81 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 27 GLU Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 76 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 316 optimal weight: 5.9990 chunk 510 optimal weight: 10.0000 chunk 311 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 354 optimal weight: 5.9990 chunk 534 optimal weight: 9.9990 chunk 492 optimal weight: 9.9990 chunk 426 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 329 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN G 8 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 ASN L 103 GLN L 192 ASN X 143 HIS ** a 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 88309 Z= 0.472 Angle : 0.960 15.053 133022 Z= 0.473 Chirality : 0.051 0.398 17149 Planarity : 0.008 0.101 6417 Dihedral : 23.485 179.971 46224 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.00 % Allowed : 23.01 % Favored : 72.99 % 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: -2.32 (0.14), residues: 2607 helix: -0.90 (0.19), residues: 629 sheet: -0.74 (0.21), residues: 592 loop : -2.25 (0.13), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP Y 65 HIS 0.010 0.002 HIS V 131 PHE 0.025 0.003 PHE Q 33 TYR 0.032 0.003 TYR V 126 ARG 0.009 0.001 ARG B 43 ********************** 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 410 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 321 time to evaluate : 3.359 Fit side-chains REVERT: A 33 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.6049 (mtt180) REVERT: D 99 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.6681 (mmtt) REVERT: F 62 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7400 (mttm) REVERT: F 71 TYR cc_start: 0.8027 (m-80) cc_final: 0.7403 (m-80) REVERT: G 17 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6662 (ttpp) REVERT: G 72 ASP cc_start: 0.6586 (OUTLIER) cc_final: 0.6274 (t0) REVERT: H 78 GLN cc_start: 0.7606 (mt0) cc_final: 0.7128 (mp10) REVERT: I 61 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7189 (ttm170) REVERT: L 61 LYS cc_start: 0.7063 (tptp) cc_final: 0.6531 (tmtp) REVERT: Q 62 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7762 (mt) REVERT: S 164 GLU cc_start: 0.5796 (tm-30) cc_final: 0.5512 (tm-30) REVERT: W 31 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6906 (ptpt) REVERT: W 67 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8323 (t) REVERT: W 97 ARG cc_start: 0.6251 (mtp180) cc_final: 0.5827 (mtp85) REVERT: X 15 GLU cc_start: 0.7176 (tt0) cc_final: 0.6896 (tt0) REVERT: Y 5 LYS cc_start: 0.7839 (mtmt) cc_final: 0.7589 (mtmm) REVERT: Z 106 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7400 (mm-40) REVERT: a 27 GLU cc_start: 0.5965 (OUTLIER) cc_final: 0.5655 (pp20) REVERT: a 90 LYS cc_start: 0.6508 (ttmm) cc_final: 0.6010 (ttpp) outliers start: 89 outliers final: 70 residues processed: 388 average time/residue: 1.7916 time to fit residues: 912.5372 Evaluate side-chains 392 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 311 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain W residue 31 LYS Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 110 ASN Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain Y residue 44 SER Chi-restraints excluded: chain Y residue 80 GLU Chi-restraints excluded: chain Y residue 81 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 27 GLU Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 76 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 338 optimal weight: 5.9990 chunk 453 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 392 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 426 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 438 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 78 optimal weight: 0.0670 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN G 8 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 ASN L 103 GLN L 167 GLN X 81 GLN X 143 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.152591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.128571 restraints weight = 79624.863| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 0.88 r_work: 0.3093 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 88309 Z= 0.269 Angle : 0.710 12.730 133022 Z= 0.364 Chirality : 0.042 0.347 17149 Planarity : 0.006 0.072 6417 Dihedral : 23.217 179.525 46224 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.69 % Allowed : 23.55 % Favored : 72.76 % 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: -1.98 (0.15), residues: 2607 helix: -0.44 (0.20), residues: 620 sheet: -0.60 (0.21), residues: 577 loop : -2.08 (0.14), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 65 HIS 0.007 0.001 HIS C 29 PHE 0.022 0.002 PHE H 79 TYR 0.024 0.002 TYR V 126 ARG 0.009 0.001 ARG E 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15266.02 seconds wall clock time: 270 minutes 45.34 seconds (16245.34 seconds total)